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Simple Summary: The gut microbiota of pigs plays an essential role in their health and growth. Observing the connections between antibiotic resistance genes, viruses, and their potential microbial hosts helps in comprehensively understanding the pig gut microbiota. This study aims to use metagenomic assembly and binning techniques to understand the distribution of antibiotic resistance genes and viruses in the pig gut microbiota and to identify possible microbial hosts. Gut microbiota plays a crucial role in the health and productivity of pigs. However, the spread of antibiotic resistance genes (ARGs) and viruses within the pig intestinal microbiota poses significant threats to animal and public health. This study utilized 181 pig samples from nine European countries and employed metagenomic assembly methods to investigate the dynamics and distribution of ARGs and viruses within the pig intestinal microbiota, aiming to observing their associations with potential bacterial hosts. We identified 4605 metagenome-assembled genomes (MAGs), corresponding to 19 bacterial phyla, 97 families, 309 genera, and a total of 449 species. Additionally, 44 MAGs were classified as archaea. Analysis of ARGs revealed 276 ARG types across 21 ARG classes, with Glycopeptide being the most abundant ARG class, followed by the class of Multidrug. Treponema D sp016293915 was identified as a primary potential bacterial host for Glycopeptide. Aligning nucleotide sequences with a viral database, we identified 1044 viruses. Among the viral genome families, Peduoviridae and Intestiviridae were the most prevalent, with CAG-914 sp000437895 being the most common potential host species for both. These findings highlight the importance of MAGs in enhancing our understanding of the gut microbiome, revealing microbial diversity, antibiotic resistance, and virus–bacteria interactions. The data analysis for the article was based on the public dataset PRJEB22062 in the European Nucleotide Archive. [ABSTRACT FROM AUTHOR]

Campylobacteriosis outbreaks have previously been linked to dairy foods. While the genetic diversity of Campylobacter is well understood in high-income countries, it is largely unknown in low-income countries, such as Ethiopia. This study therefore aimed to conduct the first genomic characterization of Campylobacter isolates from the Ethiopian dairy supply chain to aid in future epidemiological studies. Fourteen C. jejuni and four C. coli isolates were whole genome sequenced using an Illumina platform. Sequences were analyzed using the bioinformatics tools in the GalaxyTrakr platform to identify MLST types, and single nucleotide polymorphisms, and infer phylogenetic relationships among the studied isolates. Assembled genomes were further screened to detect antimicrobial resistance and virulence gene sequences. Among 14 C. jejuni, ST 2084 and ST 51, which belong to the clonal complexes ST-353 and ST-443, respectively, were identified. Among the 4 sequenced C. coli isolates, two isolates belonged to ST 1628 and two to ST 830 from the clonal complex ST-828. The isolates of C. jejuni ST 2084 and ST 51 carried β-lactam resistance gene blaOXA-605, a fluoroquinolone resistance-associated mutation T86I in the gryA gene, and a macrolide resistance-associated mutation A103V in 50S L22. Only ST 2084 isolates carried the tetracycline resistance gene tetO. Conversely, all four C. coli ST 830 and ST 1628 isolates carried tetO, but only ST 1628 isolates also carried blaOXA-605. Lastly, C. jejuni ST 2084 isolates carried a total of 89 virulence genes, and ST 51 isolates carried up to 88 virulence genes. Among C. coli, ST 830 isolates carried 71 genes involved in virulence, whereas two ST 1628 isolates carried up to 82 genes involved in virulence. Isolates from all identified STs have previously been isolated from human clinical cases, demonstrating a potential food safety concern. This finding warrants further monitoring of Campylobacter in dairy foods in Ethiopia to better understand and manage the risks associated with Campylobacter contamination and transmission. [ABSTRACT FROM AUTHOR]

High-fiber, low-cost agricultural byproducts offer a sustainable alternative for mitigating the competition for crops between humans and livestock. Pigs predominantly utilize dietary fibers through the process of microbial fermentation within the gut. This study explored the gut microbiota and the capacity for carbohydrate degradation in 30 individual Lantang pigs, a breed indigenous to China. Through metagenomic analysis, a total of 671 metagenome-assembled genomes (MAGs) were assembled and assigned into 14 bacterial and 1 archaeal phylum, including 97 species from uncultured microbes. The phylum with the highest abundance were identified as Bacillota_A, Bacteroidota, and Bacillota. Remarkably, the investigation revealed nearly 10,000 genes implicated in the degradation of carbohydrates, with a pronounced prevalence within five principal bacterial genera: Prevotella, Cryptobacteroides, Gemmiger, Vescimonas, and Faecousia. Additionally, 87 distinct types of carbohydrate-degrading enzymes were exclusively identified within the gut microbiota of the Lantang pig. These insights not only enhance our understanding of the microbial diversity specific to native Chinese pig breeds but also augment the body of research regarding porcine fiber degradation capabilities. The implications of this study are twofold: it provides strategic directions for optimizing feed efficiency and reducing breeding costs, and it furnishes an expanded gene pool for the microbial synthesis of industrial enzymes in the future. [ABSTRACT FROM AUTHOR]

The article in Liver International discusses a meta-analysis on the impact of metabolic dysfunction-associated steatotic liver disease (MASLD) and its subgroup MetALD on mortality risks. While previous studies found a positive association between MASLD and all-cause mortality, recent research suggests that systemic cardiometabolic dysfunctions, rather than steatotic liver disease itself, may be the primary factor influencing clinical outcomes in MASLD. The use of surrogate equations to diagnose steatotic liver disease may lead to misestimations and immortal time bias, highlighting the need for more accurate diagnostic processes in future studies. The authors call for further research to explore the heterogeneity of cardiometabolic risk factors in MASLD and to determine more precise management strategies for this population. [Extracted from the article]

For a broken rail detection system based on ultrasonic guided waves (UGW), the multimodal and dispersion characteristics of UGW degrade signal-to-noise ratio (SNR) and range resolution. To improve the SNR of the received signals and range resolution, the coded excitation based on Kasami sequences is presented in this work. Utilizing a PSpice model of piezoelectric ultrasonic transducers, as well as conducting field tests based on the pitch–catch mechanism, it is shown that encoded UGW signals can increase the SNRG (the gain of SNR) by 6.29 dB. The main lobe width of the coded excitation is mainly determined by the number of carrier cycles and the carrier waveform, and the size of the side lobes is mainly determined by the number of coding bits. To quickly identify the corresponding transmissions at the receivers, a peak detection algorithm is shown. It is based on bandpass filter, triangle filter and Hilbert transform. Its accuracy and effectiveness are validated by using some field tests under different distances. It can be concluded that the shown adaptive peak algorithm has strong robustness and immunity to noise. [ABSTRACT FROM AUTHOR]

Archaea are considered a "keystone" of the gut microbiome and are linked with the host's energy harvest and health. Although a few studies have investigated the gut archaea in pigs, especially piglets, little is known about the effects of weaning on archaeal structure and function. In this study, we explored the effects of weaning on the longitudinal changes of archaeal composition, diversity, and functional potential in pigs overtime by re-analyzing a recently published metagenomic dataset that included 176 fecal samples collected from commercial pigs on days 7, 14, 21, 28, 35, 70, and 140 after birth. Overall, the richness and diversity of archaeal species showed an increasing trend, and weaning significantly affected the richness of archaeal species. Methanobrevibacter A smithii significantly decreased and was replaced by Methanobrevibacter A sp900769095 within 2 weeks after weaning. For the functional potential, the richness of KEGG KOs increased over time. LEfSe analysis identified 18 KOs, including for example, ko04623 (cytosolic DNA-sensing pathway), ko00500 (starch and sucrose metabolism), and so on, significantly enriched in the weaning pigs, suggesting the involvement of archaea in the piglets' adaptation to the new diet after weaning. Correlation analysis based on Random Forest regression and Pearson correlation showed that archaeal species richness was significantly associated with pig bodyweight on both days 70 and 140. Methanobrevibacter A sp900769095 (R = 0.405, p = 0.040) and Methanobrevibacter A smithii (R = 0.535, p = 0.004) were positively linked with pigs' bodyweight on days 70 and 140, respectively. Our results revealed the dynamic changes of archaeal diversity and functions and demonstrated the effects of weaning on the gut archaea of pigs, suggesting archaea might play essential roles in swine nutrition, metabolism, and growth performance, especially during the critical weaning process. [ABSTRACT FROM AUTHOR]

Background: Compelling evidence has demonstrated the pivotal role of autophagy in the prognosis of breast cancer. Breast cancer (BC) patients with early relapse consistently exhibited worse survival. Methods: The autophagy-related genes were derived from the Human Autophagy Database (HADb) and high-sequencing data were obtained from The Cancer Genome Atlas (TCGA). Discrepantly expressed autophagy genes (DEAGs) between early relapse and long-term survival groups were performed using the Linear Models for Microarray data (LIMMA) method. Lasso Cox regression analysis was conducted for the selection of the 4-gene autophagy-related gene signature. GSE42568 and GSE21653 databases were enrolled in this study for the external validation of the signature. Then patients were divided into high and low-risk groups based on the specific score formula. GSEA was used to discover the related signaling pathway. The Kaplan-Meier curves and the receiver operating characteristic (ROC) curves were used to evaluate the discrimination and accuracy of the 4-gene signature. Results: A signature composed of four autophagy-related mRNA including APOL1, HSPA8, SIRT1, and TP73, was identified as significantly associated with the early relapse in BC patients. Time-dependent receiver-operating characteristic at 1 year suggested remarkable accuracy of the signature [area under the curve (AUC = 0.748)]. The risk score model based on the autophagy-related signature showed favorable predicting value in 1-, 2-, and 3-year relapse-free survival (RFS) in training and two validating cohorts. The GSEA displayed gene sets were remarkably enriched in carcinogenic activation pathways and autophagy-related pathways. The nomogram involving three variables (progesterone receptor status, T stage, and 4-gene signature) exhibited relatively good discrimination with a C-index of 0.766. Conclusions: Our study establishes an autophagy-related 4-gene signature that can effectively stratify the high-risk and low-risk BC patients for early relapse. Combined with the clinicopathological variables, the signature could significantly help oncologists tailor more efficient treatment strategies for BC patients. [ABSTRACT FROM AUTHOR]

This article investigates the effect of acoustic load on electromechanical characteristics of sandwiched piezoelectric ultrasonic transducers in time and frequency domains. The acoustic load includes aluminum and steel bars. It is shown that when the length of the acoustic load satisfies positive integer multiple of half-wavelength, the first resonant frequencies generate a smaller increase. With the increase of the length and characteristic impedance of acoustic load, the first resonant frequencies, and the tailing length of the received signal are increased, while the receiving signal amplitude, effective electromechanical coupling coefficient, and mechanical quality factor are decreased. [ABSTRACT FROM AUTHOR]

It is well known that exosomes could serve as anti-microbial immune factors in animals. However, despite growing evidences have shown that the homeostasis of the hemolymph microbiota was vital for immune regulation in crustaceans, the relationship between exosomes and hemolymph microbiota homeostasis during pathogenic bacteria infection has not been addressed. Here, we reported that exosomes released from Vibrio parahaemolyticus-infected mud crabs (Scylla paramamosain) could help to maintain the homeostasis of hemolymph microbiota and have a protective effect on the mortality of the host during the infection process. We further confirmed that miR-224 was densely packaged in these exosomes, resulting in the suppression of HSP70 and disruption of the HSP70-TRAF6 complex, then the released TRAF6 further interacted with Ecsit to regulate the production of mitochondrial ROS (mROS) and the expression of Anti-lipopolysaccharide factors (ALFs) in recipient hemocytes, which eventually affected hemolymph microbiota homeostasis in response to the pathogenic bacteria infection in mud crab. To the best of our knowledge, this is the first document that reports the role of exosome in the hemolymph microbiota homeostasis modulation during pathogen infection, which reveals the crosstalk between exosomal miRNAs and innate immune response in crustaceans. Author summary: Exosomes are small membrane vesicles of endocytic origin which are widely involved in the regulation of a variety of pathological processes in mammals. Yet, although the antibacterial function of exosomes has been discovered for many years, the relationship between exosomes and hemolymph microbiota homeostasis remains unknown. In the present study, we identified the miRNAs packaged by exosomes that were possibly involved in Vibrio parahaemolyticus infection by modulating hemolymph microbiota homeostasis in crustacean mud crab Scylla paramamosain. Moreover, it was found that miR-224 was densely packaged in exosomes after Vibrio parahaemolyticus challenge, resulting in the suppression of HSP70 and disruption of the HSP70-TRAF6 complex in recipient hemocytes, then the released TRAF6 was further interacted with Ecsit to regulate ROS and ALFs levels, which eventually affected hemolymph microbiota homeostasis to cope with pathogenic bacteria infection. Our finding is the first to reveal the relationship between exosomes and hemolymph microbiota homeostasis in animals, which shows a novel molecular mechanism of invertebrate resistance to pathogenic microbial infection. [ABSTRACT FROM AUTHOR]

Background: The preoperative distinguishment of lymph nodes with reactive hyperplasia or tumor metastasis plays a pivotal role in guiding the surgical extension for papillary thyroid carcinoma (PTC) with Hashimoto's thyroiditis (HT), especially in terms of the central lymph node (CLN) dissection. We aim to identify the preparative risk factors for CLN metastasis in PTC patients concurrent with HT. Materials and Methods: We retrospectively reviewed and analyzed the data including the basic information, preoperative sonographic characteristics, and thyroid function of consecutive PTC patients with HT in our medical center between Jan 2019 and Apr 2021. The Chi-square and Fisher's exact tests were used for comparison of qualitative variables among patients with or without CLN metastasis. Univariate and multivariate logistic regression analyses were used to determine the risk factors for CLN metastasis. The nomogram was constructed and further evaluated by two cohorts produced by 1,000 resampling bootstrap analysis. Results: A total of 98 in 214 (45.8%) PTC patients were identified with CLN metastasis. In multivariate analysis, four variables including high serum thyroglobulin antibody (TgAb) level (>1,150 IU/ml), lower tumor location, irregular margin of CLN, and micro-calcification in the CLN were determined to be significantly associated with the CLN metastasis in PTC patients with HT. An individualized nomogram was consequently established with a favorable C-index of 0.815 and verified via two internal validation cohorts. Conclusions: Our results indicated that preoperatively sonographic characteristics of the tumor and lymph node condition combined with serum TgAb level can significantly predict the CLN in PTC patients with HT and the novel nomogram may further help surgeons to manage the CLN in this subpopulation. [ABSTRACT FROM AUTHOR]

The mechanisms by which alcohol provokes bacterial translocation in the development of alcoholic liver disease (ALD) remain incompletely defined. Our previous study demonstrates that impaired gut epithelial antimicrobial defense is critically involved in the pathogenesis of ALD. The study was set to determine the mechanisms of how alcohol inhibits the antimicrobial ability of intestinal epithelial cells (IECs) and to explore possible solutions to this issue. C57BL/6J mice were fed either alcohol or isocaloric dextrin liquid diet for 8 weeks, and intestinal IFN-γ-signal transducer and activator of transcription (STAT) signaling was analyzed. We found that chronic alcohol exposure led to a significant reduction in intestinal IFN-γ levels compared to a control; the protein levels of phosphorylated STAT1 (p-STAT1) and p-STAT3 were both declined by alcohol. We then tested the effects of IFN-γ-STAT signaling on regulating antimicrobial peptides (AMPs), gut microbiota, and disease progression of ALD in a mouse model of chronic alcohol feeding, time-course acute IFN-γ treatment, and in vivo and in vitro IEC-specific STAT1 or STAT3 knockout mouse models, respectively. Administration of IFN-γ activated intestinal STAT1 and STAT3, upregulated the expression of Reg3 and α-defensins, orchestrated gut microbiota, and reversed alcohol-induced intestinal ZO-1 disruption and systemic endotoxin elevation as well as hepatic inflammation. Meanwhile, acute IFN-γ treatment time-dependently induced AMP expression and α-defensin activation. We then dissected the roles of STAT1 and STAT3 in this progress. Lack of IEC-specific STAT3 inhibited IFN-γ-induced expression of Reg3 and α-defensins and hindered activation of α-defensins via inactivating matrix metallopeptidase 7 (MMP7), whereas lack of IEC-specific STAT1 impaired IFN-γ-stimulated expression of α-defensins and the IEC marker, sodium-hydrogen exchanger 3. Lastly, we found that interleukin (IL)-18, a known IFN-γ inducer, was also reduced by alcohol in mice. IL-18 treatment to alcohol-fed mice normalized gut IFN-γ levels and ameliorated organ damages in both the intestine and liver. Taken together, the study reveals that IFN-γ is critically involved in the regulation of AMPs through regulation of STAT1 and STAT3; impaired IFN-γ-STAT signaling provides an explanation for alcohol-induced gut antimicrobial dysfunction and microbial dysbiosis. Therefore, IFN-γ remains a promising host defense-enhancing cytokine with unexplored clinical potential in ALD therapy. [ABSTRACT FROM AUTHOR]

LINKED CONTENT: This article is linked to Massironi et al papers. To view these articles, visit https://doi.org/10.1111/apt.16949 and https://doi.org/10.1111/apt.17552 [ABSTRACT FROM AUTHOR]

The inspection of rail defects is of importance in high-speed railway operation and maintenance. As a highly efficient method for both nondestructive testing and structural health monitoring of the rail, ultrasonic guided waves (UGWs) inspection provide increased sensitivity to smaller defects. These advantages can be fully exploited only if the complexities of UGWs propagation between the medium of air and rail are unveiled and managed for the given inspection method. The development and validation of modeling procedure for the rail based on coupled structural–acoustic model is presented in this paper. Acoustic–structure interaction between air and rail is simulated based on COMSOL Multiphysics software. The transient response and natural characteristics of UGWs in the rail was computed and predicted. Moreover, the displacement distribution of UGWs in the defective rail and nondefective rail are analyzed both in time and frequency domain. A feasible method for detecting small defects in the rail is proposed in the paper. The results indicated that a defect of 8 mm in rail head can be inspected effectively using UGWs with frequencies of 40 kHz and above. And for small defects in rail web, the X-crystallographic direction ultrasonic transducer should be chosen for inspection. [ABSTRACT FROM AUTHOR]

In a low-frequency ultrasonic guided wave dual-probe flaw inspection of a square steel bar with a finite length boundary, the flaw reflected pulse wave cannot be identified using conventional time monitoring when the flaw is located near the reflection terminal; therefore, the conventional ultrasonic echo method is not applicable and results in a non-detection zone. Using analysis and simulations of ultrasonic guided waves for the inspection of a square steel bar, the reasons for the appearance of the non-detection zone and its characteristics were analyzed and the range of the non-detection zone was estimated. Subsequently, by extending the range of the conventional detection time domain, the envelope of the specific reflected pulse signal was extracted by a combination of simulations and related envelope calculations to solve the problem of the non-detection zone in conventional inspection methods. A comparison between the simulation and the experimental results demonstrate that the solution is feasible. This study has certain practical significance for ultrasonic guided wave structural monitoring. [ABSTRACT FROM AUTHOR]

Rail defects cause numerous railway accidents. Trains are derailed and serious consequences often occur. Compared to traditional bulk wave testing, ultrasonic guided waves (UGWs) can provide larger monitoring ranges and complete coverage of the waveguide cross-section. These advantages are of significant importance for the non-destructive testing (NDT) of the continuously welded rail, and the technique is therefore widely used in high-speed railways. UGWs in continuous welded rail (CWR) and their propagation characteristics have been discussed in this paper. Finite element methods (FEMs) were used to accomplish a vibration modal analysis, which is extended by a subsequent dispersion analysis. Wave structure features were illustrated by displacement profiles. It was concluded that guided waves have the ability to detect defects in the rail via choice of proper mode and frequency. Additionally, thermal conduction that is caused by temperature variation in the rail is added into modeling and simulation. The results indicated that unbalanced thermal distribution may lead to the attenuation of UGWs in the rail. [ABSTRACT FROM AUTHOR]

Background: Few studies on cluster-based synthetic effects of multiple risk factors for birth defects have been reported. The present study aimed to identify maternal exposure clusters, explore the association between clusters of risk factors and birth defects, and further screen women with high risk for birth defects among expectant mothers.Methods: Data were drawn from a large-scale, retrospective epidemiological survey of birth defects from 2006 to 2008 in six counties of Shanxi Province, China, using a three-level stratified random cluster sampling technique. Overall risk factors were extracted using eight synthetic variables summed and examined as a total risk factor score: maternal delivery age, genetic factors, medical history, nutrition and folic acid deficiency, maternal illness in pregnancy, drug use in pregnancy, environmental risk factors in pregnancy, and unhealthy maternal lifestyle in pregnancy. Latent class cluster analysis was used to identify maternal exposure clusters based on these synthetic variables. Adjusted odds ratios (AOR) were used to explore associations between clusters and birth defects, after adjusting for confounding variables using logistic regression.Results: Three latent maternal exposure clusters were identified: a high-risk (6.15%), a moderate-risk (22.39%), and a low-risk (71.46%) cluster. The prevalence of birth defects was 14.08%, 0.85%, and 0.52% for the high-, middle- and low-risk clusters respectively. After adjusting for maternal demographic variables, women in the high-risk cluster were nearly 31 times (AOR: 30.61, 95% CI: [24.87, 37.67]) more likely to have an infant with birth defects than low-risk women.Conclusions: A high-risk group of mothers in an area with a high risk for birth defects were screened in our study. Targeted interventions should be conducted with women of reproductive age to improve neonatal birth outcomes in areas with a high risk of birth defects. [ABSTRACT FROM AUTHOR]

Environmental stress-mediated adaptation plays essential roles in the evolution of life. Cellular adaptation mechanisms usually involve the regulation of chromatin structure, transcription, mRNA stability and translation, which eventually lead to efficient changes in gene expression. Global epigenetic change is also involved in the reprogramming of somatic cells into induced pluripotent stem (iPS) cells by defined factors. Here we report that environmental stress such as hyperosmosis not only facilitates four factor-mediated reprogramming, but also enhances two or one factor-induced iPS cell generation. Hyperosmosis-induced p38 activation plays a critical role in this process. Constitutive active p38 mimics the positive effect of hyperosmosis, while dominant negative p38 and p38 inhibitor block the effect of hyperosmosis. Further study indicates stress-mediated p38 activation may promote reprogramming by reducing the global DNA methylation level and enhancing the expression of pluripotency genes. Our results demonstrate how simple environmental stress like hyperosmosis helps to alter the fate of cells via intracellular signaling and epigenetic modulation. [ABSTRACT FROM AUTHOR]

To develop a rapid detectionmethod of Staphylococcus aureus using loop-mediated isothermal amplification (LAMP), four specific primers were designed according to six distinct sequences of the nuc gene. In addition, the specificity and sensitivity of LAMP were verified and compared with those of PCR. Results showed that the LAMP reaction was completed within 45 min at 62.5°C, and ladder bands were appeared in LAMP products analyzed by gel electrophoresis. After adding 1x SYBR Green l, the positive reaction tube showed green color and the negative reaction tube remained orange, indicating that the LAMP has high specificity. The minimal detectable concentration of LAMP was 1 × 10² CFU/mL and that of PCR was 1 × 104 CFU/mL, indicating that the LAMP was 100 timesmore sensitive than the PCR. The LAMP method for detection of Staphylococcus aureus hasmany advantages, such as simple operation, high sensitivity, high specificity, and rapid analysis. Therefore, this method is more suitable for the rapid on-site detection of Staphylococcus aureus. [ABSTRACT FROM AUTHOR]