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37 pages, 1326 KB  
Review
Mitochondrial DNA Dysfunction in Cardiovascular Diseases: A Novel Therapeutic Target
by Mi Xiang, Mengling Yang, Lijuan Zhang, Xiaohu Ouyang, Alexey Sarapultsev, Shanshan Luo and Desheng Hu
Antioxidants 2025, 14(9), 1138; https://doi.org/10.3390/antiox14091138 - 21 Sep 2025
Viewed by 1068
Abstract
Cardiovascular diseases hinge on a vicious, self-amplifying cycle in which mitochondrial deoxyribonucleic acid (mtDNA) dysfunction undermines cardiac bioenergetics and unleashes sterile inflammation. The heart’s reliance on oxidative phosphorylation (OXPHOS) makes it exquisitely sensitive to mtDNA insults—mutations, oxidative lesions, copy-number shifts, or aberrant methylation—that [...] Read more.
Cardiovascular diseases hinge on a vicious, self-amplifying cycle in which mitochondrial deoxyribonucleic acid (mtDNA) dysfunction undermines cardiac bioenergetics and unleashes sterile inflammation. The heart’s reliance on oxidative phosphorylation (OXPHOS) makes it exquisitely sensitive to mtDNA insults—mutations, oxidative lesions, copy-number shifts, or aberrant methylation—that impair ATP production, elevate reactive oxygen species (ROS), and further damage the mitochondrial genome. Damaged mtDNA fragments then escape into the cytosol, where they aberrantly engage cGAS–STING, TLR9, and NLRP3 pathways, driving cytokine storms, pyroptosis, and tissue injury. We propose that this cycle represents an almost unifying pathogenic mechanism in a spectrum of mtDNA-driven cardiovascular disorders. In this review, we aim to synthesize the pathophysiological roles of mtDNA in this cycle and its implications for cardiovascular diseases. Furthermore, we seek to evaluate preclinical and clinical strategies aimed at interrupting this cycle—bolstering mtDNA repair and copy-number maintenance, reversing pathogenic methylation, and blocking mtDNA-triggered innate immune activation—and discuss critical gaps that must be bridged to translate these approaches into precision mitochondrial genome medicine for cardiovascular disease. Full article
(This article belongs to the Section Health Outcomes of Antioxidants and Oxidative Stress)
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18 pages, 1527 KB  
Article
Gene-Level Shift in Response to Synthetic Nitrogen Addition Promotes Larix olgensis (Ussurian Larch) Growth in a Short-Term Field Trial
by Muhammad Jamal Ameer, Yushan Liu, Siyu Yan and Tongbao Qu
Life 2025, 15(9), 1403; https://doi.org/10.3390/life15091403 - 4 Sep 2025
Viewed by 542
Abstract
Climate change and injudicious nitrogen addition alter the soil physico-chemical properties and microbial activity in oligotrophic forest soil, which disrupts the nitrogen cycle balance. Nevertheless, recommended fertilizer forms and levels are considered to be crucial for stable nitrogen application. We established a short-term [...] Read more.
Climate change and injudicious nitrogen addition alter the soil physico-chemical properties and microbial activity in oligotrophic forest soil, which disrupts the nitrogen cycle balance. Nevertheless, recommended fertilizer forms and levels are considered to be crucial for stable nitrogen application. We established a short-term field trial for the first time using a randomized complete block design under the yellow larch forest, with six treatments applied, including urea CO(NH2)2, ammonium chloride NH4Cl, and sodium nitrate NaNO3 at concentrations of 10 and 20 kg N hm−2 yr−1, each extended by three replicates. The gene abundances were measured using quantitative PCR (qPCR), in which the abundance levels of AOA (amoA) and nirS were higher under high CO(NH2)2 2.87 × 1010 copies g−1 dry soil and low NO3 8.82 × 109 copies g−1 dry soil, compared to CK, representing 2.8-fold and 1.5-fold increases, respectively. We found niche partitioning as revealed despite AOA (amoA) increasing in number, AOB (amoA) contributing more to ammonia oxidation while nirS proved opportunistic under stress conditions. This was supported by distinct significant correlations among factors, in which soil urease enzymatic activity (S-UE) was associated with AOA (amoA) and nirK, while AOB (amoA) and nirS positively correlated with NH4+ content and soil potential of hydrogen (pH), respectively. Among the applied treatments, high-level NO3 increased total nitrogen content and had a significant effect on soil N-acetyl-β-d-glucosaminidase (S-NAG) and soil acid protease (S-ACPT) activity. In summary, we observed an increase in Larix olgensis growth with high nitrogen retention. Full article
(This article belongs to the Special Issue Carbon and Nitrogen Cycles in Terrestrial Ecosystems)
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15 pages, 2668 KB  
Article
Cascading 58mer Alpha Satellite superHOR in Complete Orangutan Y Chromosome
by Matko Glunčić, Ines Vlahović, Marija Rosandić and Vladimir Paar
Int. J. Mol. Sci. 2025, 26(17), 8122; https://doi.org/10.3390/ijms26178122 - 22 Aug 2025
Viewed by 488
Abstract
Recent analyses have revealed that orangutan alpha satellite higher-order repeat (HOR) arrays in complete centromeres are composed of three to four distinct HOR blocks, each sharing only 80–90% sequence identity, thus forming a patchwork-quilt pattern of independent HOR expansions. In contrast, using our [...] Read more.
Recent analyses have revealed that orangutan alpha satellite higher-order repeat (HOR) arrays in complete centromeres are composed of three to four distinct HOR blocks, each sharing only 80–90% sequence identity, thus forming a patchwork-quilt pattern of independent HOR expansions. In contrast, using our novel HOR-detection algorithm GRhor, we analyzed the complete Y chromosome centromere in orangutan and identified a highly ordered and complex alpha satellite 58mer superHOR array, comprising 67 HOR copies, including 46 highly identical canonical copies with a remarkably low divergence of only 0.25%. Given that the largest known human alpha satellite HOR is the 34mer on the Y chromosome, this novel 58mer structure qualifies as a superHOR. The canonical 58mer HOR contains only 44 distinct monomer types, with 14 types repeated within the unit, resulting in a unique five-row cascading organization. Such complexity is not detectable using standard HOR-searching tools employed in previous studies. Additionally, we identified a second, less pronounced 45mer cascading superHOR array with 0.81% divergence. For comparative purposes, we also detected a cascading 18mer HOR in gorilla and a Willard-type 28mer HOR in chimpanzee Y centromeres. Notably, preliminary genome-wide analysis in orangutan reveals other superHORs, including 84mer and 53mer arrays in chromosome 5; a 54mer in chromosome 10; a 51mer in chromosome 14; a 53mer in chromosome 15; and a 45mer in chromosome 22. These findings underscore the power of GRMhor in revealing highly structured and species-specific HOR architectures, with potential implications for centromere evolution and primate comparative genomics. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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21 pages, 3049 KB  
Article
SRoFF-Yolover: A Small-Target Detection Model for Suspicious Regions of Forest Fire
by Lairong Chen, Ling Li, Pengle Cheng and Ying Huang
Forests 2025, 16(8), 1335; https://doi.org/10.3390/f16081335 - 16 Aug 2025
Viewed by 594
Abstract
The rapid detection and confirmation of Suspicious Regions of Forest Fire (SRoFF) are critical for timely alerts and firefighting operations. In the early stages of forest fires, small flames and heavy occlusion lead to low accuracy, false detections, omissions, and slow inference in [...] Read more.
The rapid detection and confirmation of Suspicious Regions of Forest Fire (SRoFF) are critical for timely alerts and firefighting operations. In the early stages of forest fires, small flames and heavy occlusion lead to low accuracy, false detections, omissions, and slow inference in existing target-detection algorithms. We constructed the Suspicious Regions of Forest Fire Dataset (SRFFD), comprising publicly available datasets, relevant images collected from online searches, and images generated through various image enhancement techniques. The SRFFD contains a total of 64,584 images. In terms of effectiveness, the individual augmentation techniques rank as follows (in descending order): HSV (Hue Saturation and Value) random enhancement, copy-paste augmentation, and affine transformation. A detection model named SRoFF-Yolover is proposed for identifying suspicious regions of forest fire, based on the YOLOv8. An embedding layer that effectively integrates seasonal and temporal information into the image enhances the prediction accuracy of the SRoFF-Yolover. The SRoFF-Yolover enhances YOLOv8 by (1) adopting dilated convolutions in the Backbone to enlarge feature map receptive fields; (2) incorporating the Convolutional Block Attention Module (CBAM) prior to the Neck’s C2fLayer for small-target attention; and (3) reconfiguring the Backbone-Neck linkage via P2, P4, and SPPF. Compared with the baseline model (YOLOv8s), the SRoFF-Yolover achieves an 18.1% improvement in mAP@0.5, a 4.6% increase in Frames Per Second (FPS), a 2.6% reduction in Giga Floating-Point Operations (GFLOPs), and a 3.2% decrease in the total number of model parameters (#Params). The SRoFF-Yolover can effectively detect suspicious regions of forest fire, particularly during winter nights. Experiments demonstrated that the detection accuracy of the SRoFF-Yolover for suspicious regions of forest fire is higher at night than during daytime in the same season. Full article
(This article belongs to the Section Natural Hazards and Risk Management)
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11 pages, 1069 KB  
Article
Evaluation of Torquetenovirus (TTV) Particle Integrity Utilizing PMAxx™
by Giuseppe Sberna, Claudia Minosse, Cosmina Mija, Eliana Specchiarello, Pietro Giorgio Spezia, Sara Belladonna, Giulia Berno, Lavinia Fabeni, Giulia Matusali, Silvia Meschi, Daniele Focosi and Fabrizio Maggi
Int. J. Mol. Sci. 2025, 26(13), 6542; https://doi.org/10.3390/ijms26136542 - 7 Jul 2025
Viewed by 815
Abstract
Torquetenovirus (TTV) is a ubiquitous, non-pathogenic DNA virus that has been suggested as a biomarker of immune competence, with the viral load correlating with the level of immunosuppression. However, by detecting non-intact viral particles, standard PCR-based quantification may overestimate the TTV viremia. To [...] Read more.
Torquetenovirus (TTV) is a ubiquitous, non-pathogenic DNA virus that has been suggested as a biomarker of immune competence, with the viral load correlating with the level of immunosuppression. However, by detecting non-intact viral particles, standard PCR-based quantification may overestimate the TTV viremia. To improve the clinical relevance of TTV quantification, in this study, we investigated the use of PMAxx™, a virion viability dye that selectively blocks the amplification of compromised virions. Serum samples from 10 Hepatitis C Virus-positive (HCV+) individuals, 81 liver transplant recipients (LTRs), and 40 people with HIV (PWH) were treated with PMAxx™ and analyzed for TTV DNA loads by digital droplet PCR (ddPCR). Furthermore, anti-SARS-CoV-2 IgG levels and neutralizing antibody (nAbs) titers were measured post-COVID-19 vaccination. Using ddPCR, the PMAxx™ treatment significantly reduced the TTV DNA levels in all the groups (mean reduction: 0.66 Log copies/mL), indicating the abundant presence of non-intact, circulating viral genomes. However, correlations between TTV DNA and SARS-CoV-2 IgG or nAbs were weak or absent in both PMAxx™-treated and untreated samples. These findings suggest that while PMAxx™ enhanced the specificity of TTV quantification, it did not improve the predictive value of TTV viremia at assessing vaccine-induced humoral responses. Full article
(This article belongs to the Section Molecular Microbiology)
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22 pages, 3253 KB  
Article
Infections of Aedes Mosquito Cells by Wolbachia Strains wAu and wMelpop Modulate Host Cellular Transcriptomes Differently and Suppress Dengue Viral Replication
by Amber R. Mickelson, Julia Felton, Olivia Cheschi, Emily Spacone, Kaitlyn Connors, Jacob Thornsberry and Tadahisa Teramoto
Viruses 2025, 17(7), 922; https://doi.org/10.3390/v17070922 - 28 Jun 2025
Viewed by 2468
Abstract
Dengue virus serotypes 1-4 (DENV1-4) have spread through tropical and subtropical countries, causing endemic and epidemic diseases. Recently, a novel field approach using the Wolbachia symbiont was proposed to suppress DENV transmission via the mosquito vectors Aedes aegypti and Aedes albopictus. Previously, [...] Read more.
Dengue virus serotypes 1-4 (DENV1-4) have spread through tropical and subtropical countries, causing endemic and epidemic diseases. Recently, a novel field approach using the Wolbachia symbiont was proposed to suppress DENV transmission via the mosquito vectors Aedes aegypti and Aedes albopictus. Previously, we showed that a Wolbachia strain, wMelPop, suppresses DENV2 replication in the C6/36 albopictus cell line, with the mutant DENV2 appearing and replacing the wild type DENV2. In this study, we expanded the analysis to include replications of all DENV serotypes 1-4, effects of wAu Wolbachia in C6/36 cells, and wMelPop-influences on the Aag2 aegypti cell line. It was revealed that both wAu and wMelPop reduce all DENV infectious titers without dominant appearances of the mutant viruses, despite varied effects on the viral copy numbers. The host transcriptomic profiles by RNA-seq were also variously altered by wAu and wMelPop (ranging from 10 to 30%, Log2FC > 2 or <−2, p < 0.05). Those transcripts were not further altered by DENV infection. In contrast, abundant transcriptomic alterations by DENV infection in naïve C6/36 and Aag2 cells were blocked by either wAu or wMelPop. These results indicate that Wolbachia prevents host cellular transcriptomic alterations which are induced by DENV infection, affecting the cellular homeostasis necessary for DENV replication. Full article
(This article belongs to the Special Issue The Impact of Wolbachia on Virus Infection)
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21 pages, 1238 KB  
Article
An In-House ELISA for Anti-Porcine Circovirus Type 2d (PCV2d) IgG: Analytical Validation and Serological Correlation
by Gyeong-Seo Park, Byoung Joo Seo, Woo Ju Kwon, Yeong Lee Seok, Hyo Jeong Lee, Sung Ho Lee, Minju Kim, MinChul Lee, Chanhee Chae and Chonghan Kim
Vaccines 2025, 13(6), 657; https://doi.org/10.3390/vaccines13060657 - 19 Jun 2025
Viewed by 809
Abstract
Background/Objectives: Porcine circovirus type 2d (PCV2d) is the predominant genotype associated with porcine circovirus-associated disease (PCVAD), leading to significant economic losses. In South Korea, current vaccine lot-release testing relies on a T/C-ratio-based guinea pig assay, which lacks scientific justification and methodological robustness. [...] Read more.
Background/Objectives: Porcine circovirus type 2d (PCV2d) is the predominant genotype associated with porcine circovirus-associated disease (PCVAD), leading to significant economic losses. In South Korea, current vaccine lot-release testing relies on a T/C-ratio-based guinea pig assay, which lacks scientific justification and methodological robustness. This study aimed to develop and validate a statistically defined in-house ELISA using rabbit-derived polyclonal antibodies against PCV2d for the standardized evaluation of immunogenicity. Methods: Polyclonal IgG was generated by immunizing a rabbit with inactivated PCV2d, and it was purified through Protein A chromatography. Guinea pigs (n = 18) were immunized with IMMUNIS® DMVac, an inactivated PCV2d vaccine candidate developed by WOOGENE B&G, at different doses. In-house ELISA parameters were optimized (antigen coating, blocking agent, and substrate incubation), and analytical performance was evaluated by ROC, linearity, reproducibility, and specificity. Sera from guinea pigs and pigs were analyzed under validated conditions. Results: The optimal performance was achieved using 105 genomic copies/mL of the antigen coating and a 5% BSA blocking agent. The assay showed strong diagnostic accuracy (AUC = 0.97), reproducibility (CVs < 5%), and linearity (R2 = 0.9890). Specificity tests with PCV2a, PCV2b, and PRRSV showed minimal cross-reactivity (<7%). The cross-species comparison revealed a positive correlation (R2 = 0.1815) and acceptable agreement (bias = −0.21) between guinea pig and porcine sera. The validated cut-off (S/P = 0.4) enabled accurate classification across both species and aligned well with commercial kits. Conclusions: The in-house ELISA offers a robust, reproducible, and scientifically validated platform for immunogenicity verification, supporting its application in Korea’s national lot-release system. Homologous competition assays with PCV2d are planned to further confirm antigen specificity. Full article
(This article belongs to the Special Issue Animal Diseases: Immune Response and Vaccines)
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12 pages, 3912 KB  
Article
A Fast and Sensitive Enzyme-Mediated Duplex Exponential Amplification Method for Field Detection of Bursaphelenchus xylophilus
by Kai Guo, Xinxin Ma, Yiwu Fang, Weijun Duan, Yao Wu, Zhenxin Hu, Weimin Ye and Jianfeng Gu
Horticulturae 2025, 11(6), 602; https://doi.org/10.3390/horticulturae11060602 - 28 May 2025
Viewed by 638
Abstract
The pinewood nematode (PWN), Bursaphelenchus xylophilus, is a pathogenic organism that causes pine wilt disease (PWD). To date, several molecular diagnostic methods have been developed; however, rapid, convenient, and inexpensive field diagnostic tools for detecting PWN are still limited. In this study, [...] Read more.
The pinewood nematode (PWN), Bursaphelenchus xylophilus, is a pathogenic organism that causes pine wilt disease (PWD). To date, several molecular diagnostic methods have been developed; however, rapid, convenient, and inexpensive field diagnostic tools for detecting PWN are still limited. In this study, an enzyme-mediated duplex exponential amplification (EmDEA) method for detecting PWN from extracted nematodes or pinewood sawdust was developed and tested. This method comprised an EmDEA molecular test kit, which consisted of freeze-dried enzyme pellets that can be stored at room temperature (approximately 20–25 °C) for one year, a dry block heater, and a portable isothermal fluorescence amplification instrument. The whole procedure was completed within 30 min. The EmDEA assay could detect a single PWN at all life stages from a mixture of other nematode species or from pinewood sawdust. The detection limit was 10 copies (plasmid weight 32.66 ag) or 1/500 of that of a single adult PWN per reaction. Therefore, the EmDEA assay has potential applications in PWN detection in the field, as well as quarantine inspection in international trade. Moreover, modification of primers and probes will allow the rapid identification of other nematode species. Full article
(This article belongs to the Special Issue Biological and Integrated Pest Management of Horticulture Crops)
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18 pages, 6877 KB  
Article
A LAMP Detection System Based on a Microfluidic Chip for Pyricularia grisea
by Chenda Wu, Jianing Cheng, Yinchao Zhang and Ping Yao
Sensors 2025, 25(8), 2511; https://doi.org/10.3390/s25082511 - 16 Apr 2025
Cited by 2 | Viewed by 763
Abstract
As one of the major rice fungal diseases, blast poses a serious threat to the yield and quality of rice globally. It is caused by the pathogen Pyricularia grisea. Therefore, the development of rapid, accurate, and portable microfluidic detection system for Pyricularia [...] Read more.
As one of the major rice fungal diseases, blast poses a serious threat to the yield and quality of rice globally. It is caused by the pathogen Pyricularia grisea. Therefore, the development of rapid, accurate, and portable microfluidic detection system for Pyricularia grisea is important for the control of rice blast. This study presents an integrated microfluidic detection system for the rapid and sensitive detection of Pyricularia grisea using the LAMP detection method. The microfluidic detection system includes a microfluidic chip, a temperature control module, and an OpenMv camera. The micro-mixing channels with shear structures improve the mixing efficiency to about 98%. Flow-blocking valves are used to reduce reagent loss in the reaction chamber. The temperature control module is used to heat the reaction chamber, maintaining a stable temperature of 65 °C. The microfluidic chip detection chamber is used for image inspection using an OpenMv camera. The developed system can detect Pyricularia grisea in the range of 10 copies/μL–105 copies/μL within 45 min. Specificity and interference experiments were performed on Pyricularia grisea, validating the method’s good reliability. This LAMP detection system based on a microfluidic chip has strong potential in the early and effective detection of rice blast. Full article
(This article belongs to the Section Smart Agriculture)
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13 pages, 1455 KB  
Article
Achieving High Efficiency and High Throughput in Erasure Code-Based Distributed Storage for Blockchain
by So-Hyun Park, So-Yeon Kim, So-Hui Kim and Il-Gu Lee
Sensors 2025, 25(7), 2161; https://doi.org/10.3390/s25072161 - 28 Mar 2025
Cited by 1 | Viewed by 945
Abstract
A blockchain is a decentralized peer-to-peer network in which all nodes store data in copies, ensuring data integrity, as transactions cannot be changed or deleted. This can lead to duplicate data storage, resulting in high storage overhead, especially in storage-constrained environments, such as [...] Read more.
A blockchain is a decentralized peer-to-peer network in which all nodes store data in copies, ensuring data integrity, as transactions cannot be changed or deleted. This can lead to duplicate data storage, resulting in high storage overhead, especially in storage-constrained environments, such as the Internet of Things (IoT) or sensor systems. Distributed storage techniques utilizing erasure code (EC) have been investigated to address this issue. Although EC-based blockchain storage increases storage efficiency, encoded chunks distributed across multiple nodes must be received to restore and access the original blocks. However, studies on increasing the data transmission efficiency of EC-based blockchain storage are limited. In this study, we propose a data transmission technique called trigger-based automatic repeat request (ARQ), enabling stable data recovery while ensuring low latency and high-throughput performance, even with frequent node failure. This technique increased the throughput efficiency by 8% while maintaining the decentralization of the blockchain. Furthermore, it maximized the storage efficiency of EC-based distributed blockchain storage by >99.8%, while solving the recovery overhead problem due to data transmission. Using the trigger-based ARQ scheme with an EC-based distribution technique, blockchains can reduce storage overhead while effectively accessing the original blocks, overcoming the limitations of conventional EC-based distributed storage. Full article
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21 pages, 7041 KB  
Article
Synergy of Internet of Things and Software Engineering Approach for Enhanced Copy–Move Image Forgery Detection Model
by Mohammed Assiri
Electronics 2025, 14(4), 692; https://doi.org/10.3390/electronics14040692 - 11 Feb 2025
Cited by 1 | Viewed by 969
Abstract
The fast development of digital images and the improvement required for security measures have recently increased the demand for innovative image analysis methods. Image analysis identifies, classifies, and monitors people, events, or objects in images or videos. Image analysis significantly improves security by [...] Read more.
The fast development of digital images and the improvement required for security measures have recently increased the demand for innovative image analysis methods. Image analysis identifies, classifies, and monitors people, events, or objects in images or videos. Image analysis significantly improves security by identifying and preventing attacks on security applications through digital images. It is crucial in diverse security fields, comprising video analysis, anomaly detection, biometrics, object recognition, surveillance, and forensic investigations. By integrating advanced software engineering models with IoT capabilities, this technique revolutionizes copy–move image forgery detection. IoT devices collect and transmit real-world data, improving software solutions to detect and analyze image tampering with exceptional accuracy and efficiency. This combination enhances detection abilities and provides scalable and adaptive solutions to reduce cutting-edge forgery models. Copy–move forgery detection (CMFD) has become possibly a major active research domain in the blind image forensics area. Between existing approaches, most of them are dependent upon block and key-point methods or integration of them. A few deep convolutional neural networks (DCNN) techniques have been implemented in image hashing, image forensics, image retrieval, image classification, etc., that have performed better than the conventional methods. To accomplish robust CMFD, this study develops a fusion of soft computing with a deep learning-based CMFD approach (FSCDL-CMFDA) to secure digital images. The FSCDL-CMFDA approach aims to integrate the benefits of metaheuristics with the DL model for an enhanced CMFD process. In the FSCDL-CMFDA method, histogram equalization is initially performed to improve the image quality. Furthermore, the Siamese convolutional neural network (SCNN) model is used to learn complex features from pre-processed images. Its hyperparameters are chosen by the golden jackal optimization (GJO) model. For the CMFD process, the FSCDL-CMFDA technique employs the regularized extreme learning machine (RELM) classifier. Finally, the detection performance of the RELM method is improved by the beluga whale optimization (BWO) technique. To demonstrate the enhanced performance of the FSCDL-CMFDA method, a comprehensive outcome analysis is conducted using the MNIST and CIFAR datasets. The experimental validation of the FSCDL-CMFDA method portrayed a superior accuracy value of 98.12% over existing models. Full article
(This article belongs to the Special Issue Signal and Image Processing Applications in Artificial Intelligence)
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16 pages, 813 KB  
Article
Impact of Feed Composition on Rumen Microbial Dynamics and Phenotypic Traits in Beef Cattle
by André L. A. Neves, Ricardo Augusto Mendonça Vieira, Einar Vargas-Bello-Pérez, Yanhong Chen, Tim McAllister, Kim H. Ominski, Limei Lin and Le Luo Guan
Microorganisms 2025, 13(2), 310; https://doi.org/10.3390/microorganisms13020310 - 31 Jan 2025
Cited by 1 | Viewed by 1498
Abstract
The rumen microbiome is central to feed digestion and host performance, making it an important target for improving ruminant productivity and sustainability. This study investigated how feed composition influences rumen microbial abundance and phenotypic traits in beef cattle. Fifty-nine Angus bulls were assigned [...] Read more.
The rumen microbiome is central to feed digestion and host performance, making it an important target for improving ruminant productivity and sustainability. This study investigated how feed composition influences rumen microbial abundance and phenotypic traits in beef cattle. Fifty-nine Angus bulls were assigned to forage- and grain-based diets in a randomized block design, evaluating microbial dynamics, methane emissions, and feed efficiency. Quantitative PCR (qPCR) quantified bacterial, archaeal, fungal, and protozoal populations. Grain-based diets reduced bacterial and fungal counts compared to forage diets (1.1 × 1011 vs. 2.8 × 1011 copies of 16S rRNA genes and 1.5 × 103 vs. 3.5 × 104 copies of 18S rRNA genes/mL, respectively), while protozoan and methanogen populations remained stable. Microbial abundance correlated with feed intake metrics, including dry matter and neutral detergent fiber intakes. Methane emissions were lower in grain-fed bulls (14.8 vs. 18.0 L CH4/kg DMI), though feed efficiency metrics showed no direct association with microbial abundance. Comparative analysis revealed adaptive microbial shifts in response to dietary changes, with functional redundancy maintaining rumen stability and supporting host performance. These findings provide insights into how feed composition shapes rumen microbial dynamics and host phenotypes, highlighting the functional adaptability of the rumen microbiome during dietary transitions. Full article
(This article belongs to the Special Issue Gut Microbiota of Food Animal)
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13 pages, 559 KB  
Review
22q11.21 Deletions: A Review on the Interval Mediated by Low-Copy Repeats C and D
by Veronica Bertini, Francesca Cambi, Annalisa Legitimo, Giorgio Costagliola, Rita Consolini and Angelo Valetto
Genes 2025, 16(1), 72; https://doi.org/10.3390/genes16010072 - 9 Jan 2025
Cited by 1 | Viewed by 1807
Abstract
22q11.2 is a region prone to chromosomal rearrangements due to the presence of eight large blocks of low-copy repeats (LCR22s). The 3 Mb 22q11.2 “typical deletion”, between LCR22-A and D, causes a fairly well-known clinical picture, while the effects of smaller CNVs harbored [...] Read more.
22q11.2 is a region prone to chromosomal rearrangements due to the presence of eight large blocks of low-copy repeats (LCR22s). The 3 Mb 22q11.2 “typical deletion”, between LCR22-A and D, causes a fairly well-known clinical picture, while the effects of smaller CNVs harbored in this interval are still to be fully elucidated. Nested deletions, flanked by LCR22B-D, LCR22B-C, or LCR22C-D, are very rare and are collectively described as “central deletions”. The LCR22C-D deletion (CDdel) has never been separately analyzed. In this paper, we focused only on CDdel, evaluating its gene content and reviewing the literature and public databases in order to obtain new insights for the classification of this CNV. At first glance, CDdels are associated with a broad phenotypic spectrum, ranging from clinically normal to quite severe phenotypes. However, the frequency of specific clinical traits highlights that renal/urinary tract abnormalities, cardiac defects, and neurological/behavioral disorders are much more common in CDdel than in the general population. This frequency is too high to be fortuitous, indicating that CDdel is a predisposing factor for these phenotypic traits. Among the genes present in this interval, CRKL is an excellent candidate for cardiac and renal defects. Even if further data are necessary to confirm the role of CDdels, according to our review, this CNV fits into the class of ‘likely pathogenic’ CNVs. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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14 pages, 2465 KB  
Article
Targeted Polymer–Peptide Conjugates for E-Selectin Blockade in Renal Injury
by Nenad Milošević, Marie Rütter, Yvonne Ventura, Valeria Feinshtein and Ayelet David
Pharmaceutics 2025, 17(1), 82; https://doi.org/10.3390/pharmaceutics17010082 - 9 Jan 2025
Cited by 1 | Viewed by 1351
Abstract
Background/Objectives: Leukocytes play a significant role in both acute kidney injury (AKI) and chronic kidney disease (CKD), contributing to pathogenesis and tissue damage. The process of leukocyte infiltration into the inflamed tissues is mediated by the interactions between the leukocytes and cell adhesion [...] Read more.
Background/Objectives: Leukocytes play a significant role in both acute kidney injury (AKI) and chronic kidney disease (CKD), contributing to pathogenesis and tissue damage. The process of leukocyte infiltration into the inflamed tissues is mediated by the interactions between the leukocytes and cell adhesion molecules (CAMs, i.e., E-selectin, P-selectin, and VCAM-1) present on the inner surface of the inflamed vasculature. Directly interfering with these interactions is a viable strategy to limit the extent of excessive inflammation; however, several small-molecule drug candidates failed during clinical translation. We hypothesized that a synthetic polymer presenting multiple copies of the high-affinity E-selecting binding peptide (P-Esbp) could block E-selectin-mediated functions and decrease leukocytes infiltration, thus reducing the extent of inflammatory kidney injury. Methods: P-Esbp was synthesized by conjugating E-selecting binding peptide (Esbp) to N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer with reactive ester groups via aminolysis. The effects of P-Esbp treatment on kidney injury were investigated in two different models: AKI model (renal ischemia—reperfusion injury—RIRI) and CKD model (adenine-induced kidney injury). Results: We found that the mRNA levels of E-selectin were up-regulated in the kidney following acute and chronic tissue injury. P-Esbp demonstrated an extended half-life time in the bloodstream, and the polymer accumulated significantly in the liver, lungs, and kidneys within 4 h post injection. Treatment with P-Esbp suppressed the up-regulation of E-selectin in mice with RIRI and attenuated the inflammatory process. In the adenine-induced CKD model, the use of the E-selectin blocking copolymer had little impact on the progression of kidney injury, owing to the compensating function of P-selectin and VCAM-1. Conclusion: Our findings provide valuable insights into the interconnection between CAMs and compensatory mechanisms in controlling leukocyte migration in AKI and CKD. The combination of multiple CAM blockers, given simultaneously, may provide protective effects for preventing excessive leukocyte infiltration and control renal injury. Full article
(This article belongs to the Special Issue Advanced Pharmaceutical Science and Technology in Israel)
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17 pages, 5365 KB  
Article
FR-IBC: Flipping and Rotation Intra Block Copy for Versatile Video Coding
by Heeji Han, Daehyeok Gwon, Jeongil Seo and Haechul Choi
Electronics 2025, 14(2), 221; https://doi.org/10.3390/electronics14020221 - 7 Jan 2025
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Abstract
Screen content has become increasingly important in multimedia applications owing to the growth of remote desktops, Wi-Fi displays, and cloud computing. However, these applications generate large amounts of data, and their limited bandwidth necessitates efficient video coding. While existing video coding standards have [...] Read more.
Screen content has become increasingly important in multimedia applications owing to the growth of remote desktops, Wi-Fi displays, and cloud computing. However, these applications generate large amounts of data, and their limited bandwidth necessitates efficient video coding. While existing video coding standards have been optimized for natural videos originally captured by cameras, screen content has unique characteristics such as large homogeneous areas and repeated patterns. In this paper, we propose an enhanced intra block copy (IBC) method for screen content coding (SCC) in versatile video coding (VVC) named flipping and rotation intra block copy (FR-IBC). The proposed method improves the prediction accuracy by using flipped and rotated versions of the reference blocks as additional references. To reduce the computational complexity, hash maps of these blocks are constructed on a 4 × 4 block size basis. Moreover, we modify the block vectors and block vector predictor candidates of IBC merge and IBC advanced motion vector prediction to indicate the locations within the available reference area at all times. The experimental results show that our FR-IBC method outperforms existing SCC tools in VVC. Bjøntegaard-Delta rate gains of 0.66% and 2.30% were achieved under the All Intra and Random Access conditions for Class F, respectively, while corresponding values of 0.40% and 2.46% were achieved for Class SCC, respectively. Full article
(This article belongs to the Section Circuit and Signal Processing)
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