Correlation of caecal microbiome endotoxins genes and intestinal immune cells in Eimeria tenella infection based on bioinformatics

IntroductionThe infection with Eimeria tenella (ET) can elicit expression of various intestinal immune cells, incite inflammation, disrupt intestinal homeostasis, and facilitate co-infection with diverse bacteria. However, the reciprocal interaction between intestinal immune cells and intestinal flora in the progression of ET-infection remains unclear.ObjectiveThe aim of this study was to investigate the correlation between cecal microbial endotoxin (CME)-related genes and intestinal immunity in ET-infection, with subsequent identification of hub potential biomarker and immunotherapy target.MethodsDifferential expression genes (DEGs) within ET-infection and hub genes related to CME were identified through GSE39602 dataset based on bioinformatic methods and Protein-protein interaction (PPI) network analysis. Moreover, immune infiltration was analyzed by CIBERSORT method. Subsequently, comprehensive functional enrichment analyses employing Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis along with Gene Ontology (GO), gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA) were performed.ResultsA total of 1089 DEGs and 25 hub genes were identified and CXCR4 was ultimately identified as a essential CME related potential biomarker and immunotherapy target in the ET-infection. Furthermore, activated natural killer cells, M0 macrophages, M2 macrophages, and T regulatory cells were identified as expressed intestinal immune cells. The functional enrichment analysis revealed that both DEGs and hub genes were significantly enriched in immune-related signaling pathways.ConclusionCXCR4 was identified as a pivotal CME-related potential biomarker and immunotherapy target for expression of intestinal immune cells during ET-infection. These findings have significant implications in elucidating the intricate interplay among ET-infection, CME, and intestinal immunity

NTIRE 2024 Quality Assessment of AI-Generated Content Challenge

This paper reports on the NTIRE 2024 Quality Assessment of AI-Generated Content Challenge, which will be held in conjunction with the New Trends in Image Restoration and Enhancement Workshop (NTIRE) at CVPR 2024. This challenge is to address a major challenge in the field of image and video processing, namely, Image Quality Assessment (IQA) and Video Quality Assessment (VQA) for AI-Generated Content (AIGC). The challenge is divided into the image track and the video track. The image track uses the AIGIQA-20K, which contains 20,000 AI-Generated Images (AIGIs) generated by 15 popular generative models. The image track has a total of 318 registered participants. A total of 1,646 submissions are received in the development phase, and 221 submissions are received in the test phase. Finally, 16 participating teams submitted their models and fact sheets. The video track uses the T2VQA-DB, which contains 10,000 AI-Generated Videos (AIGVs) generated by 9 popular Text-to-Video (T2V) models. A total of 196 participants have registered in the video track. A total of 991 submissions are received in the development phase, and 185 submissions are received in the test phase. Finally, 12 participating teams submitted their models and fact sheets. Some methods have achieved better results than baseline methods, and the winning methods in both tracks have demonstrated superior prediction performance on AIGC

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Disagreements in risk of bias assessment for randomized controlled trials in hypertension-related Cochrane reviews

Abstract Background The inter-reviewer reliability of the risk of bias (RoB) assessment lacked agreement in previous studies. It is important to analyse these disagreements to improve the repeatability of RoB assessment. The objective of the study was to evaluate the frequency and reasons for disagreements in RoB assessments for randomised controlled trials (RCTs) that were included in multiple Cochrane reviews in the field of hypertension. Methods A cross-sectional study was employed. We retrieved any RCTs that had been included in multiple Cochrane reviews in the field of hypertension from ARCHIE. The results of the RoB assessments were extracted, and the distributions of agreements and possible reasons for disagreement were analyzed. Results Twenty-six Cochrane reviews were included in this study. A total of 78 RCTs appeared in more than one Cochrane review. The level of agreement ranged from domain to domain. “Blinding of outcome assessment” showed a reasonably high level of agreement (94.9%), while “incomplete outcome data”, “selective outcome reporting” and “other sources of bias” showed moderate levels of agreement (74.6%, 79.2% and 75.6%, respectively). However, the domains of “allocation concealment”, “random sequence generation” and “blinding of participants and personnel” showed low levels of agreement (24.4%, 23.5%, and 47.4%, respectively). In the domains of “allocation concealment” and “blinding of participants and personnel”, the agreement group had higher proportion of publication year ≤ 1996 than the disagreement group (P = 0.008 and P < 0.001, respectively). In the “blinding of participants and personnel”, the impact factor was higher in the agreement group (P < 0.001). By analyzing the support text, we found that the most likely reason for disagreement was extracting different information from the same RCT. Conclusion For Cochrane reviews in the field of hypertension using the 2011 version of the RoB tool, there was a large disagreement in the RoB assessment. It is suggested that the results of RoB assessments in systematic reviews that used the 2011 version of the RoB tool need to be interpreted with caution. More accurate information from RCTs needs to be collected when we synthesize clinical evidence

Arsenic and antimony co-induced nephrotoxicity via autophagy and pyroptosis through ROS-mediated pathway in vivo and in vitro

Arsenic (As) and antimony (Sb) are commonly accumulated environmental pollutants that often coexist in nature and cause serious widespread biological toxicity. To investigate the nephrotoxicity induced by As and Sb in detail, we explored the mechanism by which As and Sb cotreatment induced autophagy and pyroptosis in vivo and in vitro. In this study, mice were treated with 4 mg/kg arsenic trioxide (ATO) or/and 15 mg/kg antimony trichloride (SbCl3) by intragastric intubation for 60 days. TCMK-1 cells were treated with ATO (12.5 μM), SbCl3 (25 μM) or a combination of As and Sb for 24 h. The results of the in vivo experiment demonstrated that As or/and Sb exposure could induce histopathological changes in the kidneys, and increase the levels of biochemical indicators of nephrotoxicity. In addition, As and Sb can co-induce oxidative stress, which further activate autophagy and pyroptosis. In an in vitro experiment, As and/or Sb coexposure increased ROS generation and decreased MMP. Moreover, the results of related molecular experiments further confirmed that As and Sb coactivated autophagy and pyroptosis. In conclusion, our results indicated that As and Sb co-exposure could cause autophagy and pyroptosis via the ROS pathway, and these two metals might have a synergistic effect on nephrotoxicity

Copper induces mitochondria-mediated apoptosis via AMPK-mTOR pathway in hypothalamus of Pigs

Copper (Cu), one of the heavy metals, is far beyond the carrying capacity of the environment with Cu mining, industrial wastewater discharging and the use of Cu-containing pesticides. Intaking excess Cu can cause toxic effects on liver, kidney, heart, but few studies report Cu toxicity on brain tissue. It is noteworthy that most toxicity tests are based on rodent models, but large mammals chosen as animal models has no reported. To explore the relationship of the Cu toxicity and mitochondria-mediated apoptosis on hypothalamus in pigs, the content of Cu, histomorphology, mitochondrial related indicators, apoptosis, and AMPK-mTOR signaling pathway were detected. Results showed that Cu could accumulate in hypothalamus and lead to mitochondrial dysfunction, evidenced by the decrease of ATP production, activities of respiratory chain complex I-IV, and mitochondrial respiratory function in Cu-treated groups. Additionally, the genes and proteins expression of Bax, Caspase-3, Cytc in treatment group were higher than control group. Furthermore, the protein level of p-AMPK was enhanced significantly and p-mTOR was declined, which manifested that AMPK-mTOR signaling pathway was activated in Cu-treated groups. In conclusion, this study illuminated that the accumulation of Cu could cause mitochondrial dysfunction, induce mitochondria-mediated apoptosis and activate AMPK-mTOR pathway in hypothalamus