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Bacterial biofilms are organized heterogeneous assemblages of microbial cells encased within a self-produced matrix of exopolysaccharides, extracellular DNA and proteins. Over the last decade, more and more biofilm-associated proteins have been discovered and investigated. Furthermore, omics techniques such as transcriptomes, proteomes also play important roles in identifying new biofilm-associated genes or proteins. However, those important data have been uploaded separately to various databases, which creates obstacles for biofilm researchers to have a comprehensive access to these data. In this work, we constructed BBSdb, a state-of-the-art open resource of bacterial biofilm-associated protein. It includes 48 different bacteria species, 105 transcriptome datasets, 21 proteome datasets, 1205 experimental samples, 57,823 differentially expressed genes (DEGs), 13,605 differentially expressed proteins (DEPs), 1,930 'Top 5% differentially expressed genes', 444 'Threshold-based DEGs' and a predictor for prediction of biofilm-associated protein. In addition, 1,781 biofilm-associated proteins, including annotation and sequences, were extracted from 942 articles and public databases via text-mining analysis. We used E. coli as an example to represent how to explore potential biofilm-associated proteins in bacteria. We believe that this study will be of broad interest to researchers in field of bacteria, especially biofilms, which are involved in bacterial growth, pathogenicity, and drug resistance. Availability and implementation: The BBSdb is freely available at http://124.222.145.44/#!/., Competing Interests: The authors declare that no financial support was received for the research, authorship, and/or publication of this article. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Zhang, Pan, Hussain, Chen and Li.)

Background: Pre-operative prediction of postoperative nausea and vomiting (PONV) is primarily based on the patient's medical history. The predictive value of gastric morphological parameters observed on ultrasonography has not been comprehensively assessed., Methods: A prospective observational study was conducted to evaluate the pre-operative ultrasonographic measurement of gastric morphology for predicting PONV. The gastric antrum of the participants was assessed using ultrasound before anesthesia, and the occurrence of PONV in the first 6 hours and during the 6-24 hours after surgery was reported. The main indicators included the thickness of the muscularis propria (TMP) and the cross-sectional area of the inner side of the muscularis propria (CSA-ISMP). These were recorded and analyzed. Logistic regression analysis was applied to identify factors for PONV., Results: A total of 72 patients scheduled for elective gynecological laparoscopic surgery were investigated in the study. The pre-operative CSA-ISMP of patients with PONV in the first 6 hours was significantly greater than that of those without PONV (2.765 ± 0.865 cm² vs 2.349 ± 0.881 cm², P=0.0308), with an area under the curve of 0.648 (95% CI, 0.518 to 0.778, P=0.031). Conversely, the pre-operative TMP of patients with PONV during the 6-24 hours was significantly smaller than that of those without PONV (1.530 ± 0.473 mm vs 2.038 ± 0.707 mm, P=0.0021), with an area under the curve of 0.722 (95% CI, 0.602 to 0.842, P=0.003). Logistic regression analysis confirmed that CSA-ISMP was an independent risk factor for PONV in the first 6 hours (OR=2.986, P=0.038), and TMP was an independent protective factor for PONV during the 6-24 hours after surgery (OR=0.115, P=0.006)., Conclusion: Patients with a larger pre-operative CSA-ISMP or a thinner TMP are prone to develop PONV in the first 6 hours or during the 6-24 hours after surgery, respectively., China Clinical Trial Registration Center: http://www.chictr.org.cn (ChiCTR2100055068)., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Qiu, Yin, Liang, Shi, Liu, Zhang, Bai, Chen and Xiong.)

Most of vaccinees and COVID-19 convalescents can build effective anti-SARS-CoV-2 humoral immunity, which helps preventing infection and alleviating symptoms. However, breakthrough viral infections caused by emerging SARS-CoV-2 variants, especially Omicron subvariants, still pose a serious threat to global health. By monitoring the viral infections and the sera neutralization ability of a long-tracked cohort, we found out that the immune evasion of emerging Omicron subvariants and the decreasing neutralization led to the mini-wave of SARS-CoV-2 breakthrough infections. Meanwhile, no significant difference had been found in the infectivity of tested SARS-CoV-2 variants, even though the affinity between human angiotensin-converting enzyme 2 (hACE2) and receptor-binding domain (RBDs) of tested variants showed an increasing trend. Notably, the immune imprinting of inactivated COVID-19 vaccine can be relieved by infections of BA.5.2 and XBB.1.5 variants sequentially. Our data reveal the rising reinfection risk of immune evasion variants like Omicron JN.1 in China, suggesting the importance of booster with updated vaccines., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Liu, Jin, Mei, Fan, Gu, Zhang, Qian, Tan, Ji, Zhang, Chen, Yan, Chen, Lan, Geng, Cai and Zhou.)

The rapid reversal of deep neuromuscular blockade (NMB) is important but remains challenging. This study aimed to evaluate the efficacy and safety of adamgammadex versus sugammadex in reversing deep rocuronium-induced NMB. This multicenter, randomized, phase IIb study included 80 patients aged 18-64 years, American Society of Anesthesiologists (ASA) grade 1-2, undergoing elective surgery under general anesthesia with rocuronium. Patients were randomized to the adamgammadex 7, 8, and 9 mg/kg group or the sugammadex 4 mg/kg group. The primary efficacy variable was the time to recovery of train-of-four ratio (TOFr) to 0.9. The secondary efficacy variables were the time to recovery of TOFr to 0.7, antagonistic success rate of the recovery of TOFr to 0.9 within 5 min, and incidence rate of recurarization within 30 min after drug administration. The explorative efficacy variable was the time to recovery of the corrected TOFr to 0.9 (actual/baseline TOF ratio). Adamgammadex 7, 8, and 9 mg/kg and sugammadex 4 mg/kg groups did not significantly differ in all efficacy variables. Importantly, adamgammadex 9 mg/kg permitted reversal within a geometric mean of 2.9 min. According to the safety profile, adamgammadex achieved good tolerance and low incidence of drug-related adverse events compared with the 4 mg/kg sugammadex. Adamgammadex 7, 8, and 9 mg/kg facilitated rapid reversal of deep rocuronium-induced NMB and had good tolerance and low incidence of drug-related adverse events. Therefore, adamgammadex is a potential and promising alternative to sugammadex., (© 2024 The Authors. Clinical and Translational Science published by Wiley Periodicals LLC on behalf of American Society for Clinical Pharmacology and Therapeutics.)

Introduction: Using black soldier fly larvae (BSFLs) to treat food waste is one of the most promising environmental protection technologies., Methods: We used high-throughput sequencing to study the effects of different nutritional compositions on the intestinal microbiota and digestive enzymes of BSF., Results: Compared with standard feed (CK), high-protein feed (CAS), high-fat feed (OIL) and high-starch feed (STA) had different effects on the BSF intestinal microbiota. CAS significantly reduced the bacterial and fungal diversity in the BSF intestinal tract. At the genus level, CAS, OIL and STA decreased the Enterococcus abundance compared with CK, CAS increased the Lysinibacillus abundance, and OIL increased the Klebsiella , Acinetobacter and Bacillus abundances. Diutina , Issatchenkia and Candida were the dominant fungal genera in the BSFL gut. The relative abundance of Diutina in the CAS group was the highest, and that of Issatchenkia and Candida in the OIL group increased, while STA decreased the abundance of Diutina and increased that of Issatchenkia . The digestive enzyme activities differed among the four groups. The α-amylase, pepsin and lipase activities in the CK group were the highest, and those in the CAS group were the lowest or the second lowest. Correlation analysis of environmental factors showed a significant correlation between the intestinal microbiota composition and digestive enzyme activity, especially α-amylase activity, which was highly correlated with bacteria and fungi with high relative abundances. Moreover, the mortality rate of the CAS group was the highest, and that of the OIL group was the lowest., Discussion: In summary, different nutritional compositions significantly affected the community structure of bacteria and fungi in the BSFL intestinal tract, affected digestive enzyme activity, and ultimately affected larval mortality. The high oil diet gave the best results in terms of growth, survival and intestinal microbiota diversity, although the digestive enzymes activities were not the highest., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Chen, Zhang, Tang, Li, Pang, Yuan, Song, Jiang, Yu, Zhu, Wang, Zhang and Zhang.)

Microbial aerosols in intensive broiler houses whose species and concentrations are closely related to human health are ubiquitous. Based on 16S rRNA gene sequencing, the aim of this study was to investigate the spatial distribution and diversity of bacterial aerosols in the air of broiler houses. Significant spatial variations in airborne bacterial concentrations were observed inside the poultry farmhouse. The results indicated that bacteria in the air samples could be grouped into a total of 1,674 OTUs. Alpha diversity analysis showed that the diversity of the microbial community at the entry of the broiler house was higher than that at the middle or the rear ( p < 0.01). The Sankey diagram illustrated species dynamic changes in Proteobacteria , Firmicutes , and Actinobacteria among the different locations. From the aspect of LEfSe (LDA Effect Size) analysis, we discovered that the abundance of Planctomycetes was significantly higher in the entry than in the rear and middle. This study shows the spatial distribution of the entire bacterial community in intensive broiler houses, which offers a new perspective for studying airborne total bacteria in those environments. Implications: The bacteria contained in air aerosols from poultry houses are closely connected to animal health and production. This study aimed to investigate the spatial distribution and diversity of bacterial aerosols in the air of broiler houses. The results observed that bacterial aerosol concentrations in the examined broilers house varied greatly at different positions, and a significantly higher exposure to bacterial aerosol was observed at the middle than at the other positions (p < 0.05). The alpha diversity analysis showed that the diversity of the microbial community at the entry of the broiler house was higher than that at the middle or the rear (P<0.01). Sankey diagram illustrated species dynamic changes of Proteobacteria, Firmicutes and Actinobacteria among the different locations. The microbial communities in genus level in the samples of entry and rear were closer, while the species diversity of middle and rear samples in chicken house was highly similar (P>0.05). Altogether, results revealed that the effects of spatial factors on the diversity and abundance of bacteria in the air of closed-cage broiler houses, which poses a potential threat to the health of animals and workers in those environments.

As one of the most successful pathogenic organisms, Vibrio cholerae (V. cholerae) has evolved sophisticated regulatory mechanisms to overcome host stress. During long-term colonization by V. cholerae in adult mice, many spontaneous nonmotile mutants (approximately 10% at the fifth day post-infection) were identified. These mutations occurred primarily in conserved regions of the flagellar regulator genes flrA, flrC, and rpoN, as shown by Sanger and next-generation sequencing, and significantly increased fitness during colonization in adult mice. Intriguingly, instead of key genes in DNA repair systems (mutS, nfo, xthA, uvrA) or ROS and RNS scavenging systems (katG, prxA, hmpA), which were generally thought to be associated with bacterial mutagenesis, we found that deletion of the cyclin gene dps significantly increased the mutation rate (up to 53% at the fifth day post-infection) in V. cholerae. We further determined that the dpsD65A and dpsF46E point mutants showed a similar mutagenesis profile as the Δdps mutant during long-term colonization in mice, which strongly indicated that the antioxidative function of Dps directly contributes to the development of V. cholerae nonmotile mutants. Methionine metabolism pathway may be one of the mechanism for ΔflrA, ΔflrC and ΔrpoN mutant increased colonization in adult mice. Our results revealed a new phenotype in which increased fitness of V. cholerae in the host gut via spontaneous production nonmotile mutants regulated by cyclin Dps, which may represent a novel adaptation strategy for directed evolution of pathogens in the host., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Luo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Atopic dermatitis (AD) is a chronic inflammatory cutaneous disorder in which the skin is affected by microbial dysbiosis. The role of commensal skin microbiota in AD is of great interest. Extracellular vesicles (EVs) are important regulators of skin homeostasis and pathology. The mechanism of preventing AD pathogenesis through commensal skin microbiota-derived EVs remains poorly understood. In this study, we investigated the role of commensal skin bacterium Staphylococcus epidermidis-derived EVs (SE-EVs). We showed that SE-EVs significantly decreased the expression of proinflammatory genes (TNFα, IL1β, IL6, IL8, and iNOS) through lipoteichoic acid and increased the proliferation and migration of calcipotriene (MC903)-treated HaCaT cells. Furthermore, SE-EVs increased the expression of human β-defensins 2 and 3 in MC903-treated HaCaT cells through toll-like receptor 2, enhancing resistance to S. aureus growth. In addition, topical SE-EV application remarkably attenuated inflammatory cell infiltration (CD4 + T cells and Gr1 + cells), T helper 2 cytokine gene expression (Il4, Il13, and Tlsp), and IgE levels in MC903-induced AD-like dermatitis mice. Intriguingly, SE-EVs induced IL-17A + CD8 + T-cell accumulation in the epidermis, which may represent heterologous protection. Taken together, our findings showed that SE-EVs reduced AD-like skin inflammation in mice and may potentially be a bioactive nanocarrier for the treatment of AD., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

We present the complete genome sequence of an aviadenovirus obtained by metagenomics from cloacal swabs taken from a free-living Eurasian scops owl (Otus scops, a small raptor distributed in Europe and several parts of Asia) in China. Thirty protein coding genes were predicted in this 40,239-bp-long genome, which encodes the largest fiber protein among all reported aviadenoviruses. The viral genome sequence is highly divergent, and the encoded proteins have an average of only 55% amino acid sequence identity to those of other adenoviruses. In phylogenetic analysis, the new owl virus grouped with members of the genus Aviadenovirus and formed a common clade with another owl adenovirus reported previously in Japan. This is the second complete genome sequence of an aviadenovirus discovered in owls, and its proteins have an average of 62% amino acid sequence identity to those of the previously reported owl adenovirus. Combining this result with comparative genomic analysis of all aviadenoviruses, we propose that this owl virus and the previously described Japanese owl adenovirus can be assigned to two new species in the genus Aviadenovirus. This study provides new data on the diversity of aviadenoviruses in wild birds., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

Mr.Vc is a database of curated Vibrio cholerae transcriptome data and annotated information. The main objective is to facilitate the accessibility and reusability of the rapidly growing Vibrio cholerae omics data and relevant annotation. To achieve these goals, we performed manual curation on the transcriptome data and organized the datasets in an experiment-centric manner. We collected unknown operons annotated through text-mining analysis that would provide more clues about how Vibrio cholerae modulates gene regulation. Meanwhile, to understand the relationship between genes or experiments, we performed gene co-expression analysis and experiment-experiment correlation analysis. In additional, functional module named "Interactions" which dedicates to collecting experimentally validated interactions about Vibrio cholerae from public databases, MEDLINE documents and literature in life science journals. To date, Mr.Vc v2, which is significantly increased from the previous version, contains 107 microarray experiments, 106 RNA-seq experiments, and 3 Tn-seq projects, covering 56,839 entries of DEGs (Differentially Expressed Genes) from transcriptomes and 7,463 related genes from Tn-seq, respectively. and a total of 270,129 gene co-expression entries and 11,990 entries of experiment-experiment correlation was obtained, in total 1,316 entries of interactions were collected, including 496 protein-chemical signaling molecule interactions, 472 protein-protein interactions, 306 TF (Transcription Factor)-gene interactions and 42 Vibrio cholerae -virus interactions, most of which obtained from 402 literature through text-mining analysis. To make the information easier to access, Mr.Vc v2 is equipped with a search widget, enabling users to query what they are interested in. Mr.Vc v2 is freely available at http://mrvcv2.biownmc.info., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Zhang, Chen, Hussain, Qin, Liu, Su, Zhang and Ye.)

The bacteria contained in air aerosols from poultry houses are closely connected to animal health and production. This study aimed to investigate the seasonal factors on microbial aerosol concentration, particle size and bacterial spectrum composition inside a closed-cage broiler house. Then, 16S rDNA sequencing technology was applied to analyze the characteristics of bacterial abundance and diversity. The results indicated that the concentration of bacterial aerosol in the broiler house varied significantly in different seasons, with a concentration range of 5.87-15.77 × 10 3 CFU/m 3 , and the highest and lowest concentrations in the summer and winter, respectively. Microbiological analysis showed that the proportion of Gram-negative bacteria in autumn was significantly higher than that in summer ( P < 0.05). In addition, the floral structure of potential pathogenic bacterial genera also differed by season. Escherichia-Shigella, Streptococcus, Acinetobacter, Pseudomonas were identified in the bacterial aerosols. Importantly, the relative abundance of Firmicutes in spring and autumn was much higher. In contrast, the relative abundance of Proteobacteria in spring and autumn was lower than that in summer and winter. Altogether, results revealed the effects of seasonal factors on the diversity and abundance of bacteria and the distribution characteristics of major opportunistic pathogens in the air of closed-cage broiler houses. These results will provide important information for exploring the potential risk of aerosols from poultry houses all four seasons., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Chen, Yan, Xiu, Jiang, Zhang, Chen, Yu, Zhu, Zhao, Li, Tang and Zhang.)

Objective: To investigate the clinical predictive value of combined diaphragmatic and pulmonary ultrasound in acute respiratory failure patients with mechanical ventilation (MV)., Methods: From January 2020 to August 2022, patients with acute respiratory failure admitted to People's Hospital Affiliated to Ningbo University who underwent invasive MV and weaning were enrolled. After meeting the weaning standards, spontaneous breathing test (SBT) was performed using T-tube. Right diaphragm excursion (DE), diaphragm thickness and lung ultrasound score (LUS) were collected by bedside ultrasound at 30 minutes of SBT, and rapid shallow respiratory index (RSBI), diaphragmatic-shallow respiratory index (D-RSBI) and diaphragmatic thickening rate (DTF) were calculated. According to the weaning outcome, the patients were divided into successful weaning group and failed weaning group. The clinical data of all patients were collected, and the ultrasound parameters and clinical indicators were compared between the two groups. Receiver operator characteristic curve (ROC curve) was used to evaluate the predictive value of D-RSBI, RSBI, DE combined with LUS score and DTF combined with LUS score for weaning failure patients., Results: A total of 77 patients were enrolled, including 54 cases in the successful weaning group and 23 cases in the failed weaning group. The right DE and DTF of patients in successful weaning group were significantly higher than those in failed weaning group [right DE (cm): 1.28±0.39 vs. 0.88±0.41, DTF: (32.64±18.27)% vs. (26.43±15.23)%, both P < 0.05], LUS score, RSBI and D-RSBI were significantly lower than those in failed weaning group [LUS score: 11.45±2.67 vs. 18.33±3.62, RSBI (times×min -1 ×L -1 ): 72.21±19.67 vs. 107.35±21.32, D-RSBI (times×min -1 ×mm -1 ): 0.97±0.19 vs. 1.78±0.59, all P < 0.05]. ROC curve analysis showed that when the cut-off value of D-RSBI and RSBI was 1.41 times×min -1 ×mm -1 and 56.46 times×min -1 ×L -1 , the area under the ROC curve (AUC) for predicting weaning failure was 0.972 and 0.988; and the sensitivity was 95.7% and 87.0%, respectively; the specificity was 81.0% and 100.0%, respectively. The AUC of right DE combined with LUS score and DTF combined with LUS score in predicting weaning failure were 0.974 and 0.985, respectively, with a sensitivity of 91.3% and a specificity of 98.1%., Conclusions: Combined assessment of diaphragmatic and pulmonary ultrasound is a good parameter to effectively predict weaning failure in MV patients, which has high application value in guiding weaning in MV patients, and is worthy of clinical application.

Circular RNAs (circRNAs) are aberrantly expressed in the brain and play a role in a variety of central nervous system diseases. However, the essential role and therapeutic potential of circRNAs in ischemic stroke (IS) are poorly understood. Here, using circRNA sequencing, we showed that circRNA homeodomain-interacting protein kinase 3 (circHIPK3) was abundantly expressed in ischemic brain tissues in transient middle cerebral artery occlusion (tMCAO)-evoked stroke model mice. Knockdown of circHIPK3 markedly reduced the infarct volume, brain water content, neurological deficit scores, and blood-brain permeability and ameliorated brain microvascular endothelial cell (BMEC) apoptosis and mitochondrial dysfunction in tMCAO mice. Gain- and loss-of-function experiments were performed to verify the effects of miR-148b-3p on oxygen-glucose deprivation (OGD)-induced BMEC apoptosis and mitochondrial dysfunction. Mechanistically, circHIPK3 functions as an endogenous sponge of miR-148b-3p to decrease its activity, resulting in upregulation of CDK5R1 and CDK5 expression, downregulation of SIRT1 expression and subsequent BMEC apoptosis and mitochondrial dysfunction. Collectively, our findings suggest that circHIPK3 and its coupling mechanism are implicated in IS, providing translational evidence that circHIPK3 could be a key therapeutic target for IS., (Copyright © 2022. Published by Elsevier Inc.)

The changes of microbial communities of rhizospheric soil in different ages are speculated to cause soil-borne diseases and replanting problem in American ginseng (Panax quinquefolius L.) cultivation. This study analyzed the physicochemical properties and microbial communities of rhizospheric soil during the planting of American ginseng in the Wendeng area of Weihai, China. The water content and organic matter content of American ginseng rhizospheric soil decreased year by year. A decline in the diversity of bacteria and fungi was observed in the rhizospheric soils planting American ginseng compared with the traditional crop wheat in the control group. During the later planting stage, the abundances of Proteobacteria, Actinobacteria, and Basidiomycota were lower, whereas that of Acidobacteria, Firmicutes, and Mucoromycota were higher. Through the correlation analysis between environmental factors and microbial community, it was found that the content of soil phosphorus was significantly positively correlated with the root rot pathogen Fusarium. The results of functional prediction showed that the decrease of secondary metabolite synthesis of rhizospheric soil bacteria and the increase of plant pathogenic fungi may be the important reasons for the increase of diseases in the later stage of American ginseng planting. This study revealed the evolution of rhizosphere microbial community and function in the process of American ginseng planting, which is valuable for planting management., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

We present the first complete genome sequence of an aviadenovirus Oriolus adenovirus (OrAdV) sequenced from the cloaca of a Oriolus chinensis (a passerine bird widely distributed in Asia), which was collected from an island off the east coast of China. Thirty-one protein coding genes were predicted in this 40425-bp-long genome. OrAdV genome is highly divergent and has only 57% average protein identity compared with other aviadenovirus genomes. Comparative genomic analysis indicates that this passerine virus is a new species of aviadenovirus. One unique thymidylate kinase gene was discovered in OrAdV genome. This gene is absent in other adenovirus genomes and usually reported to occur in herpesvirus. Protein sequence alignment against all known proteins indicates that this gene may be originated from ancient horizontal gene transfer event between virus and parasitic eukaryote like protozoan. This new aviadenovirus genome enriches the genomic information of adenovirus and suggests that there is a large unknown space of adenovirus world., (Copyright © 2022. Published by Elsevier B.V.)

The gut microbiome profile of COVID-19 patients was found to correlate with a viral load of SARS-CoV-2, COVID-19 severity, and dysfunctional immune responses, suggesting that gut microbiota may be involved in anti-infection. In order to investigate the role of gut microbiota in anti-infection against SARS-CoV-2, we established a high-throughput in vitro screening system for COVID-19 therapeutics by targeting the endoribonuclease (Nsp15). We also evaluated the activity inhibition of the target by substances of intestinal origin, using a mouse model in an attempt to explore the interactions between gut microbiota and SARS-CoV-2. The results unexpectedly revealed that antibiotic treatment induced the appearance of substances with Nsp15 activity inhibition in the intestine of mice. Comprehensive analysis based on functional profiling of the fecal metagenomes and endoribonuclease assay of antibiotic-enriched bacteria and metabolites demonstrated that the Nsp15 inhibitors were the primary bile acids that accumulated in the gut as a result of antibiotic-induced deficiency of bile acid metabolizing microbes. This study provides a new perspective on the development of COVID-19 therapeutics using primary bile acids., Competing Interests: YSD and LH are employed by KMHD, Shenzhen, China. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Ma, Luo, Deng, Yang, Wang, Chen, Qin, Deng, Nan, Chen, Wang, Wei, Han, Fang and Liu.)

Objective: Activation of PI3K pathway has been reported to promote survival, tumorigenicity and metastasis in the esophageal cancer (EC), and the PI3Kp110β (one of PI3K family) contributed to tumorigenesis in types of cancers. However, it is still unclear whether PI3Kp110β effects the progression of EC., Methods: RT-qPCR and western blot were used to detect the expression of PI3Kp110β in the patients with EC and ECA-109 cells transfected with si-PI3Kp110β. CCK-8 and clonogenic assays were performed to analyze the proliferation of ECA-109 cells. Flow cytometry was used to investigate cell cycle and apoptosis of ECA-109 cells., Results: The expression of PI3Kp110β was up-regulated in the patients with EC by online RNA Sep data and RT-qPCR assay. Compared with the ECA-109 cells with si-control, the proliferation was suppressed in the ECA-109 cells with si-PI3Kp110β. The G1 phase of the cells with si-PI3Kp110β was significantly higher than that of cells with si-control. The apoptosis of cells with si-PI3Kp110β was accelerated, compared with that of cells with si-control. The expression of cyclinD1 and Bcl-2 was decreased, while the expression of Bax was increased in the ECA-109 cells with si-PI3Kp110β., Conclusion: Inhibition of si-PI3Kp110β attenuates cell viability and enhances apoptosis in esophageal cancer., (© 2022 by the Association of Clinical Scientists, Inc.)

Background: To investigate the relationship between fluid-attenuated inversion recovery (FLAIR) vascular hyperintensity (FVH), hemodynamics, and functional outcome in atherosclerotic middle cerebral artery (MCA) stenosis using a computational fluid dynamics (CFD) model based on magnetic resonance angiography (MRA), according to a modified Rankin Scale (mRS) at 3 months., Methods: A total of 120 patients with 50-99% atherosclerotic MCA stenosis were included. The training and internal validation groups were composed of 99 participants and 21 participants, respectively. Demographic, imaging data, and functional outcome (mRS at 3 months) were collected. Hemodynamic parameters were obtained from the CFD model. The FVH score was based on the number of territories where FVH is positive, according to the spatial distribution in the Alberta Stroke Program Early Computed Tomography Score (ASPECTS). The prediction models were constructed according to clinical and hemodynamic parameters using multivariate logistic analysis. The DeLong test compared areas under the curves (AUCs) of the models., Results: The multivariable logistic regression analysis showed that the National Institute of Health Stroke Scale (NIHSS) at admission, hypertension, hyperlipidemia, the ratio of wall shear stress before treatment (WSSR before ), and difference in the ratio of wall shear stress (WSSR) were independently associated with functional outcome (all P<0.05). In the training group before treatment, the AUC of model 1a (only clinical variables) and 2a (clinical variables with addition of WSSR before ) were 0.750 and 0.802. After treatment, the AUC of model 1b (only clinical variables) and 2b (clinical variables with addition of difference in WSSR) were 0.815 and 0.883, respectively. The AUC of models with hemodynamic parameters was significantly higher than the models based on clinical variables only (all P<0.05, DeLong test). In the internal validation group before treatment, the AUC of the model (clinical variables) was 0.782, and that of the model (clinical variables and WSSR before ) was 0.800. After treatment, the AUC of the model (clinical variables) was 0.833, and that of the model (clinical variables and difference in WSSR) was 0.861. There were no significant differences between the good and the poor functional outcome group concerning FVH before scores before treatment (0.30±0.81 vs. 0.26±0.97; P=0.321) and FVH after scores after treatment (0.08±0.39 vs. 0.00±0.00; P=0.244)., Conclusions: Hemodynamics was associated with functional outcomes in patients with ischemic stroke attributed to atherosclerotic MCA stenosis, while FVH was not. Hemodynamic parameters were of great importance in the prediction models., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://dx.doi.org/10.21037/qims-21-337). The authors have no conflicts of interest to declare., (2022 Quantitative Imaging in Medicine and Surgery. All rights reserved.)

This study aims to verify the time-variant feature of American ginseng (AG) continuous cropping obstacles and to explore the factors impeding continuous cropping. We verified the feature with a plant-soil feedback pot experiment and then investigated the factors by comparing the properties of control soils that had not been previously used for growing ginseng (CS) with those of soils with a 10-year-crop-rotation cycle following the growth of AG (RS). It's found that the survival rate of AG in RS was lower than that in CS. The RS had lower pH, available potassium content, and urease activity. Additionally, p-coumaric, p-hydroxybenzoic, vanillic, caffeic, and cinnamic acid levels were lower in RS than in CS, but salicylic acid levels showed the opposite pattern. RS had higher Rhodanobacter and lower Acidothermus, Sphingomonas relative abundances in bacterial community. It's also found that many bacteria were substantially correlated with phenolic acids and soil physiochemical properties. Results indicate that even after 10-year crop rotation, the negative effects of prior continuous cropping of AG has not been eliminated. The growth of AG can be affected negatively with deterioration of soil physicochemical properties and with lower levels of phenolic acids which promote pathogen reproduction. Probiotics reduction also weighs. Moreover, biotic factors are interrelated with abiotic ones. Therefore, it can be inferred that the comprehensive change of soil properties is the main obstacle for continuous cropping.

Using black soldier fly (Hermetia illucens) larvae in treatment of livestock manure is a promising technology. In this study, high-throughput sequencing was used to analyze the microbial community in chicken manure before and after treatment with H. illucens larvae. In fresh chicken manure, the most abundant bacterial phylum was Firmicutes (55.58%) followed by Bacteroidetes (24.52%) and then Proteobacteria (12.29%). After treatment of the manure with H. illucens larvae for 15 days, the abundance of Firmicutes increased to 97.72% while that of Bacteroidetes and Proteobacteria decreased. Concomitantly, the most abundant genera of fungi in chicken manure changed from Kernia (46.19%) and Microascus (17.22%) to Penicillium (46.82%) and Aspergillus (45.22%). Correlation-network analysis showed the existence of strong and complex correlations between the dominant operational taxonomic units (OUT) of bacteria and fungi. While most of these correlations were positive, three specific genera, namely g&#95;norank&#95;f&#95;Bacillaceae, Penicillium, and Aspergillus exhibited negative correlations with the remaining genera. These three genera were highly abundant in the intestines of H. illucens and in chicken manure treated with H. illucens larvae. Based on 16S rDNA microbiome-function predictions, the metabolic pathways associated with sugars, amino acids, and organic pollutants inside the intestinal tract of H. illucens were enriched versus those of the other three groups. In summary, the treatment of chicken manure with H. illucens larvae significantly reduced the microbial diversity, while strongly increasing organic metabolism in the intestinal bacteria. This technology shows the potential for applications in livestock manure treatment.

Objectives: To build models based on conventional logistic regression (LR) and machine learning (ML) algorithms combining clinical, morphological, and hemodynamic information to predict individual rupture status of unruptured intracranial aneurysms (UIAs), afterwards tested in internal and external validation datasets., Methods: Patients with intracranial aneurysms diagnosed by computed tomography angiography and confirmed by invasive cerebral angiograph or clipping surgery were included. The prediction models were developed based on clinical, aneurysm morphological, and hemodynamic parameters by conventional LR and ML methods., Results: The training, internal validation, and external validation cohorts were composed of 807 patients, 200 patients, and 108 patients, respectively. The area under curves (AUCs) of conventional LR models 1 (clinical), 2 (clinical and aneurysm morphological), and 3 (clinical, aneurysm morphological and hemodynamic characteristics) were 0.608, 0.765, and 0.886, respectively (all p < 0.05). The AUCs of ML models using random forest (RF), multilayer perceptron (MLP), and support vector machine (SVM) were 0.871, 0.851, and 0.863, respectively. There were no difference among AUCs of conventional LR, RF, and SVM (all p > 0.05/6), while the AUC of MLP was lower than that of conventional LR (p = 0.0055)., Conclusion: Hemodynamic parameters play an important role in the prediction performance of the models. ML methods cannot outperform conventional LR in prediction models for rupture status of UIAs integrating clinical, aneurysm morphological, and hemodynamic parameters., Key Points: • The addition of hemodynamic parameters can improve prediction performance for rupture status of unruptured intracranial aneurysms. • Machine learning algorithms cannot outperform conventional logistic regression in prediction models for rupture status integrating clinical, aneurysm morphological, and hemodynamic parameters. • Models integrating clinical, aneurysm morphological, and hemodynamic parameters may help choose the optimal management.

Purpose: The aim of the study was to investigate the diagnostic accuracy of peri-thrombus vascular hyperintensity sign (PVHS) on three-dimensional (3D) black-blood (BB) contrast-enhanced MRI for the detection of intracranial thrombus location and length in acute ischemic stroke (AIS) patients., Materials and Methods: Consecutive AIS patients who underwent MRI including 3D BB contrast-enhanced MRI sequence within 8 h of clinical onset were prospectively evaluated. Two readers independently reviewed the 3D BB contrast-enhanced MRI data to assess the presence and location of PVHS. Findings were compared with those of contrast-enhanced MR angiography (CE-MRA) as the reference standard., Results: The PVHS was identified in 49% (63/129) of AIS patients with good agreement. The PVHS had 100% specificity, 88% negative predictive value, 89% sensitivity, and 100% positive predictive value for detection of acute arterial occlusions. Eight patients showed discordant thrombus locations between 3D BB contrast-enhanced MRI and CE-MRA. Median thrombus length in patients with complete occlusion was 9.61 mm., Conclusion: The PVHS on 3D BB contrast-enhanced MRI is a highly specific tool for evaluating the location and length of a thrombus in AIS patients.

Objective: To evaluate the value of lung ultrasonography score (LUS) on assessing extravascular lung water (EVLW) and prognosis in patients with acute respiratory distress syndrome (ARDS)., Methods: The clinical data of 46 patients meeting ARDS Berlin definition admitted to intensive care unit (ICU) of Ningbo Yinzhou People's Hospital from July 2016 to December 2019 were retrospectively collected. The general data, vital signs, blood lactic acid (Lac), oxygenation index (OI), LUS, extravascular lung water index (EVLWI), sequential organ failure assessment (SOFA) score, clinical pulmonary infection score (CPIS) and the length of ICU stay were collected. According to the prognosis of patients during ICU treatment, the patients were divided into survival group and non-survival group, and the clinical characteristics between the two groups were compared. The correlation between LUS and OI, EVLWI, SOFA, and CPIS were analyzed by Pearson correlation analysis. Receiver operator characteristic (ROC) curve was plotted to determine the prognostic value of LUS for ARDS patients during ICU treatment., Results: Forty-six patients were enrolled in the analysis, of whom 32 patients survived (69.6%), and 14 patients died (30.4%) during ICU treatment. There was no significant difference in gender, age, left ventricular ejection fraction (LVEF) or heart rate (HR) between the two groups. Compared with the survival group, the mean arterial pressure (MAP) and OI in the non-survival group were significantly lowered [MAP (mmHg, 1 mmHg = 0.133 kPa): 57.48±33.34 vs. 85.45±19.56, OI (mmHg): 74.50±18.40 vs. 233.06±28.28, both P < 0.05], while Lac, LUS, EVLWI, SOFA and CPIS were significantly increased [Lac (mmol/L): 6.78±2.56 vs. 2.21±1.42, LUS score: 23.57±2.03 vs. 15.58±2.24, EVLWI (mL/kg): 22.93±2.56 vs. 12.96±2.18, SOFA score: 20.21±3.35 vs. 12.43±2.97, CPIS score: 8.07±1.38 vs. 4.59±1.04, all P < 0.01], and the length of ICU stay was significantly shortened (days: 9.33±3.28 vs. 16.89±4.12, P < 0.05]. Pearson correlation analysis showed that a significant negative linear correlation was found between LUS and OI (r = -0.823, P < 0.01), and positive linear correlations were found between LUS and EVLWI, SOFA, CPIS (r values were 0.745, 0.614, 0.757, respectively, all P < 0.01). ROC curve analysis showed that both LUS and EVLWI could predict the prognosis of ARDS patients during ICU treatment, and the areas under ROC curve (AUC) of LUS and EVLWI were 0.936 and 0.991, respectively. When the cut-off of LUS score was 20.5, the sensitivity and specificity were 85.7% and 81.2% respectively., Conclusions: LUS score has a good correlation with EVLWI monitored by pulse index continuous cardiac output (PiCCO), which can reflect lung water content. LUS score can be used as an early prognostic indicator for ARDS patients.

Members of marine Actinobacteria have been highly regarded as potentially important sources of antimicrobial compounds. Here, we isolated a strain of Actinobacteria, SZJ61, and showed that it inhibits the in vitro growth of fungi pathogenic to plants. This new isolate was identified as Streptomyces luteoverticillatus by morphological, biochemical and genetic analyses. Antifungal compounds were isolated from S. luteoverticillatus strain SZJ61 and characterized as carbazomycin B by nuclear magnetic resonance spectra. We then sequenced the genome of the S. luteoverticillatus SZJ61 strain, which consists of only one 7,367,863 bp linear chromosome that has a G+C content of 72.05%. Thirty-five putative biosynthetic gene clusters for secondary metabolites, including a variety of bioactive products, were found. Mining of the genome sequence information revealed the putative biosynthetic gene cluster of carbazomycin B. This genomic information is valuable for interpreting the biosynthetic mechanisms of diverse bioactive compounds that have potential applications in the pharmaceutical industry.

L-aspartate-α-decarboxylase was extracellularly expressed to enhance its production for β-alanine biosynthesis. L-aspartate-α-decarboxylase and cutinase were coexpressed in Escherichia coli; more than 40% of the L-aspartate-α-decarboxylase was secreted into the medium. Selection of best conditions among tested variables enhanced L-aspartate-α-decarboxylase production by the recombinant strain. The total L-aspartate-α-decarboxylase activity reached 20.3 U/mL. Analysis of the enzymatic properties showed that the optimum temperature and pH for L-aspartate-α-decarboxylase were 60 °C and 7.5, respectively. Enzyme activity was stable at pH 4.0-8.5 and displayed sufficient thermal stability at temperatures < 50 °C. In addition, enzymatic synthesis of β-alanine was performed using extracellularly expressed L-aspartate-α-decarboxylase, and a mole conversion rate of > 99% was reached with a substrate concentration of 1.5 M. Extracellular expression of L-aspartate-α-decarboxylase resulted in increased enzyme production, indicating its possible application in the enzymatic synthesis of β-alanine.

We developed a regulatable gene expression system for Vibrio vulnificus, which contains a lacIq-pTrc cassette. Monomeric red fluorescence protein (mRFP) was used as a reporter to test this system. The results showed that this system tightly controlled the expression of mRFP without leaky expression and was suitable for the controlled expression of genes encoding recombinant proteins in V. vulnificus. To demonstrate the utility of this system, a dominant negative form of V. vulnificus VVMO6&#95;RS04990, a homolog of Escherichia coli LolD that is essential in lipoprotein transport and membrane biogenesis, was inducibly expressed. Expression of the dominant negative LolD homolog, which has a mutation in the ATPase domain, resulted in a growth defect in V. vulnificus cells and impaired cell envelope stability. This result suggests that the V. vulnificus LolD homolog plays a role in cell envelope biogenesis. This tight and titratable expression system will therefore be a valuable tool for the study of essential genes in V. vulnificus.

Methane is reported to have antioxidant, anti-inflammatory and anti-apoptotic properties. We investigated the potential neuroprotective effects of methane-rich saline (MS) on spinal cord ischemia-reperfusion injury and determined that its therapeutic benefits are associated with the activation of nuclear factor erythroid 2-related factor 2 (Nrf2). Rats received 9min of spinal cord ischemia induced by occlusion of the descending thoracic aorta plus systemic hypotension followed by a single MS treatment (10ml/kg, ip) and 72h reperfusion. MS treatment attenuated motor sensory deficits and produced high concentrations of methane in spinal cords during reperfusion, which increased Nrf2 expression and transcriptional activity in neurons, microglia and astrocytes in the ventral, intermediate and dorsal gray matter of lumbar segments. Heme oxygenase-1, superoxide dismutase, catalase and glutathione were upregulated; and glutathione disulfide, superoxide, hydrogen peroxide, malondialdehyde, 8-hydroxy-2-deoxyguanosine and 3-nitrotyrosine were downregulated in MS-treated spinal cords. MS treatment reduced neuronal apoptosis in gray matter zones, which was consistent with the suppression of cytochrome c release to the cytosol from the mitochondria and the activation of caspase-9 and -3. Throughout the gray matter, the activation of microglia and astrocytes was inhibited; the nuclear accumulation of phosphorylated nuclear factor-kappa B p65 was reduced; and tumor necrosis factor α, interleukin 1β, chemokine (C-X-C motif) ligand 1, intercellular adhesion molecule 1 and myeloperoxidase were decreased. MS treatment attenuated blood-spinal cord barrier dysfunction by preventing the expression and activity of matrix metallopeptidase-9 and disrupting tight junction proteins. Consecutive intrathecal injection of specific siRNAs targeting Nrf2 at 24-h intervals 3 days before ischemia reduced the beneficial effects of MS. Our data indicate that MS treatment prevents IR-induced spinal cord damage via antioxidant, anti-inflammatory and anti-apoptotic activities that involve the activation of Nrf2 signaling. Thus, methane may serve as a novel promising therapeutic agent for treating ischemic spinal cord injury., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Background: In recent decades, morbidity and mortality have been found to be significantly increased in patients with chronic obstructive pulmonary disease (COPD) complicated with pulmonary tuberculosis (PTB). Platelet-lymphocyte ratio (PLR) is an indicator for inflammatory diseases. This study aims to investigate whether PLR could act as a potential marker for patients with COPD complicated with PTB., Methods: In this retrospective study, laboratory characteristics of 87 COPD patients complicated with PTB (determined by Mycobacterium tuberculosis positive culture from sputum or bronchial lavage fluid) and 83 COPD patients (as the control group, determined by M. tuberculosis culture negativity from sputum or bronchial lavage fluid) were investigated. Data obtained on the day of admission were analyzed., Results: PLR >216.82 was identified as the optimal cutoff value for discriminating COPD patients with PTB (sensitivity 92.4%, specificity 84.5%, positive-predictive value 91.6%, negative-predictive value 86.2%, and area under the curve [AUC] was 0.87) from patients with COPD alone. The AUC of PLR was significantly greater than that of neutrophil-lymphocyte count ratio (AUC, 0.74; 95% confidence interval, 0.67-0.81; P <0.01)., Conclusion: PLR could be developed as a valuable maker for identifying tuberculosis infection in COPD patients., Competing Interests: The authors report no conflicts of interest in this work.

Objective: We screened bacteria producing L-aspartate α-decarboxylase from grapery soil and optimized the fermentation conditions., Methods: L-aspartate α-decarboxylase producing bacteria were screened by color-changing circle and liquid secondary screening culture media. Combination of morphological, physiological and biochemical characteristics and 16S rRNA sequence analysis were used to identify the bacteria. Fermentation conditions were optimized by single factor test and orthogonal experiment., Results: Strain PanD37 showed high L-aspartate α-decarboxylase producing property and was identified as Bacillus tequilensis. The optimum fermentation conditions of PanD37 were liquid volume of 50 mL in 500 mL flask, 220 r/min at 35 °C, inoculation amount of 5% for 28 h with a medium of 22.5 g/L sucrose, 7.5 g/L fumaric acid, 20 g/L peptone, 6 g/L L-aspartic acid, 2 g/L Triton X-100, at initial pH of 7.0. Under the optimal fermentation conditions, the highest L-aspartate α-decarboxylase activity reached 44.57 U/mL, which was 2.57 folds higher than that obtained before optimization., Conclusion: Strain PanD37 was identified as Bacillus tequilensiswhich was capable of highly producing L-aspartate α-decarboxylase under the optimal fermentation conditions.

Background and Aim: TFF1 (pS2) is expressed at a high level in gastric epithelial cells and plays an important role in protecting the gastric mucosa. However, the regulatory mechanisms of TFF1 expression are not fully understood. The aim of this study was to investigate the effect of TNF-alpha, a representative proinflammatory cytokine, on TFF1 expression., Methods: MKN45 and AGS cells, derived from human gastric carcinoma, were used. Endogenous TFF1 mRNA expression was analyzed by real-time quantitative RT-PCR. The sequences of the human TFF1 promoter were cloned into the pGL3-basic vector and reporter gene assays were performed. Nuclear factor (NF)-kappaB activity was monitored using a reporter vector that contained multiple copies of NF-kappaB responsive element upstream of the luciferase gene. Interaction between NF-kappaB and TFF1 cis-element was examined by electophoretic mobility shift assay (EMSA)., Results: TNF-alpha activated NF-kappaB and up-regulated endogenous TFF1 mRNA expression as well as the transcription of the TFF1 reporter genes in a dose-dependent manner. IL-1beta, another proinflammatory cytokine, also up-regulated TFF1 expression. TNF-alpha responsive element was mapped between -342 and -147 of the human TFF1 promoter and a putative NF-kappaB binding site was identified at -231. When this element was deleted, the reporter genes became almost insensitive to TNF-alpha treatment. EMSA showed binding of NF-kappaB to this element., Conclusions: Inflammatory stimuli that activate NF-kappaB appear to up-regulate TFF1 expression in gastric epithelial cells. This mechanism may aid in the protection of the gastric mucosa under inflammatory conditions.