Engineered CRISPR RNA improves the RNA cleavage efficiency of hfCas13X.

As the most compact variant in the Cas13 family, CRISPR-Cas13X holds considerable promise for gene therapy applications. The development of high-fidelity Cas13X (hfCas13X) mutants has enhanced the safety profile for in vivo applications. However, a notable reduction in on-target cleavage efficiency accompanies the diminished collateral cleavage activity in hfCas13X. In this study, we obtained two engineered crRNA mutants that notably enhance the on-target cleavage efficiency of hfCas13X. Furthermore, we have identified a novel crRNA structure that consistently augments the on-target cleavage efficiency of hfCas13X across various cellular environments, without significant enhancement of its collateral activity. These findings collectively enrich the gene-editing toolkit, presenting a more effective hfCas13X system for future research and application.

Apelin (APLN) is a biomarker contributing to the diagnosis and prognosis of hepatocellular carcinoma.

Liver cancer, classified as a malignant hepatic tumor, can be divided into two categories: primary, originating within the liver, and secondary, resulting from metastasis to the liver from other organs. Hepatocellular carcinoma (HCC) is the main form of primary liver cancer and the third leading cause of cancer-related deaths. The diagnosis and prognosis of HCC using current methods still face numerous challenges. This study aims to develop novel diagnostic and prognostic models while identifying new biomarkers for improved HCC treatment. Diagnostic and prognostic models for HCC were constructed using traditional binary classification methods and machine learning algorithms based on the TCGA database (Downloaded in August 2023). The mechanisms by which APLN (Apelin) affects HCC were investigated using single-cell sequencing data sourced from the GEO database (GSE149614). The diagnostic models yielded by various algorithms could effectively distinguished HCC samples from normal ones. The prognostic model, composed of four genes, was constructed using LASSO and Cox regression algorithms, demonstrating good performance in predicting the three-year survival rate of HCC patients. The HCC biomarker Apelin (APLN) was identified in this study. APLN in liver cancer tissues mainly comes from endothelial cells and is associated with the carcinogenesis of these cells. APLN expression is significantly upregulated in liver cancer tissues, marking it as a viable indicator of endothelial cell malignancy in HCC. Furthermore, APLN expression was determined to be an independent predictor of tumor endothelial cell carcinogenesis, unaffected by its modifications such as single nucleotide variation, copy number variation, and methylation. Additionally, liver cancers characterized by high APLN expression are likely to progress rapidly after T2 stage. Our study presents diagnostic and prognostic models for HCC with appreciably improved accuracy and reliability compared to previous reports. APLN is a reliable HCC biomarker and contributes to the establishment of our models.

Advancing microRNA target site prediction with transformer and base-pairing patterns.

MicroRNAs (miRNAs) are short non-coding RNAs involved in various cellular processes, playing a crucial role in gene regulation. Identifying miRNA targets remains a central challenge and is pivotal for elucidating the complex gene regulatory networks. Traditional computational approaches have predominantly focused on identifying miRNA targets through perfect Watson-Crick base pairings within the seed region, referred to as canonical sites. However, emerging evidence suggests that perfect seed matches are not a prerequisite for miRNA-mediated regulation, underscoring the importance of also recognizing imperfect, or non-canonical, sites. To address this challenge, we propose Mimosa, a new computational approach that employs the Transformer framework to enhance the prediction of miRNA targets. Mimosa distinguishes itself by integrating contextual, positional and base-pairing information to capture in-depth attributes, thereby improving its predictive capabilities. Its unique ability to identify non-canonical base-pairing patterns makes Mimosa a standout model, reducing the reliance on pre-selecting candidate targets. Mimosa achieves superior performance in gene-level predictions and also shows impressive performance in site-level predictions across various non-human species through extensive benchmarking tests. To facilitate research efforts in miRNA targeting, we have developed an easy-to-use web server for comprehensive end-to-end predictions, which is publicly available at http://monash.bioweb.cloud.edu.au/Mimosa.

Dynamic measurement for the impact of project portfolio synergy.

Measuring the impact of project portfolio synergy (PPSI) is crucial for making informed decisions to improve the strategic realization of a project portfolio. However, the literature has failed to measure PPSI effectively from the perspective of project element flow and to explore the differences in synergy relationships between homogeneous and heterogeneous projects. Consequently, this study proposes a framework for measuring PPSI from the perspective of project element flow. First, based on analyzing the synergistic relationship between projects, the corresponding project element datum quantity is determined according to the different types of element flow forms. Second, the synergy degree between homogeneous and heterogeneous projects is quantified through project similarity and correlation. Third, a dynamic measurement model is constructed using System Dynamics to solve the complex interactive feedback and dynamics in the PPSI measurement system. Finally, the framework is demonstrated and validated by a numerical example of project management in Xi'an, Shaanxi Province. The results indicate that the model can effectively measure PPSI and identify the key factors generating it. In implementing the portfolio, managers must focus on sharing and integrating newly developed technologies and information, thus facilitating the generation of PPSI. This study extends the boundary of project portfolio synergy theory and contributes to the literature on measuring PPSI by focusing on the elements flow within portfolios. Additionally, the model provides an effective tool for managers to forecast PPSI and determine appropriate optimization strategies.

Design, synthesis, and biological activity evaluation of dihydromyricetin derivatives against SARS-CoV-2-Omicron virus.

An oxidising and substituting one-pot reaction strategy has been developed to synthesise dihydromyricetin derivatives with the aim of enhancing the inhibitory activity of dihydromyricetin against SARS-CoV-2. Different ω-methoxy-ω-oxeylkyl was introduced in C7-OH site and yielded eight analogs, all of them showed good inhibitory activity against SARS-CoV-2 3CLpro with IC50 values ranging from 0.72 to 2.36 µM. In the Vero E6-cell, compound 3 has a good activity of anti-SARS-CoV-2 virus (Omicron virus BA.5) in the prevention model, with an EC50 of 15.84 µM, and so do compound 10 in the therapeutic model, with an EC50 of 11.52 µM. The results suggest that the introduction of long chain ω-oxeylkyl at C7-OH facilitate the inhibition of viral replication in the therapeutic model, which is consistent with the binding energies predicted from molecular docking conclusions. It implies that dihydromyricetin derivatives have the potential to become effective inhibitors of SARS-CoV-2 Omicron and other viruses.

Glioma-Stem-Cell-Derived Exosomes Remodeled Glioma-Associated Macrophage via NEAT1/miR-125a/STAT3 Pathway.

Glioblastoma (GBM), as the most common primary brain tumor, usually results in an extremely poor prognosis, in which glioma stem cells (GSCs) and their immunosuppressive microenvironment prominently intervene in the resistance to radiotherapy and chemotherapy that directly leads to tumor recurrence and shortened survival time. The specific mechanism through which exosomes generated from GSCs support the creation of an immunosuppressive microenvironment remains unknown, while it is acknowledged to be engaged in intercellular communication and the regulation of the glioma immunosuppressive microenvironment. The elevated expression of LncRNA-NEAT1 was found in glioma cells after radiotherapy, chemotherapy, and DNA damage stimulation, and NEAT1 could promote the malignant biological activities of GSCs. Emerging evidence suggests that lncRNAs may reply to external stimuli or DNA damage by playing a role in modulating different aspects of tumor biology. Our study demonstrated a promotive role of the carried NEAT1 by GSC-derived exosomes in the polarization of M2-like macrophages. Further experiments demonstrated the mediative role of miR-125a and its target gene STAT3 in NEAT1-induced polarization of M2-like macrophages that promote glioma progression. Our findings elucidate the mechanism by which GSCs influence the polarization of M2-like macrophages through exosomes, which may contribute to the formation of immunosuppressive microenvironments. Taken together, our study reveals the miR-125a-STAT3 pathway through which exosomal NEAT1 from treatment-resistant GSCs contributes to M2-like macrophage polarization, indicating the potential of exosomal NEAT1 for treating glioma.

The value of ripple mapping in the age of coherent mapping in scar-related atrial tachycardia.

BACKGROUND: An accurate display of scar-related atrial tachycardia (ATs) is a key determinant of ablation success. The efficacy of ripple mapping (RM) in identifying the mechanism and critical isthmus of scar-related ATs during coherent mapping is unknown. METHODS: A total of 97 patients with complex ATs who underwent radiofrequency catheter ablation at our center between October 2018 and September 2022 were included. ATs was mapped using a multielectrode mapping catheter on the CARTO3v7 CONFIDENCE module. Coherent and RM were used to identify the reentrant circuit. RESULTS: The mechanisms of 128 ATs were analyzed retrospectively (84 anatomic-reentrant ATs and 44 non-anatomic reentrant ATs). The median AT cycle length was 264 ± 25ms. The correct diagnosis was achieved in 83 ATs (68%) using only coherent mapping. Through coherent mapping plus RM, 114 ATs (84.2%) were correctly diagnosed (68% vs. 89%, p = .019). In non-anatomical reentrant ATs, 81% of the diagnostic rate was achieved by reviewing both coherent and ripple mapping compared to reviewing coherent mapping alone (81% vs. 52%, p = .03). Reviewing coherent mapping and ripple mapping showed a higher diagnostic rate in patients who underwent cardiac surgery than those with Coherent mapping alone (64% vs. 88%, p = .04). CONCLUSION: Coherent mapping combined with RM was superior to coherent mapping alone in identifying the mechanism of scar-related ATs post-cardiac surgery and non-anatomic reentrant ATs.

Alpha-Lipoic Acid Induces Adipose Tissue Browning through AMP-Activated Protein Kinase Signaling in Vivo and in Vitro.

Background: AMP-activated protein kinase (AMPK) is a key enzyme for cellular energy homeostasis and improves metabolic disorders. Brown and beige adipose tissues exert thermogenesis capacities to dissipate energy in the form of heat. Here, we investigated the beneficial effects of the antioxidant alpha-lipoic acid (ALA) in menopausal obesity and the underlying mechanisms. Methods: Female Wistar rats (8 weeks old) were subjected to bilateral ovariectomy (Ovx) and divided into four groups: Sham (n=8), Ovx (n=11), Ovx+ALA2 (n=10), and Ovx+ALA3 (n=6) (ALA 200 and 300 mg/kg/day, respectively; gavage) for 8 weeks. 3T3-L1 cells were used for in vitro study. Results: Rats receiving ALA2 and ALA3 treatment showed significantly lower levels of body weight and white adipose tissue (WAT) mass than those of the Ovx group. ALA improved plasma lipid profiles including triglycerides, total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol. Hematoxylin & eosin staining of inguinal WAT showed that ALA treatment reduced Ovx-induced adipocyte size and enhanced uncoupling protein 1 (UCP1) expression. Moreover, plasma levels of irisin were markedly increased in ALA-treated Ovx rats. Protein expression of brown fat-specific markers including UCP1, PRDM16, and CIDEA was downregulated by Ovx but markedly increased by ALA. Phosphorylation of AMPK, its downstream acetyl-CoA carboxylase, and its upstream LKB1 were all significantly increased by ALA treatment. In 3T3-L1 cells, administration of ALA (100 and 250 µM) reduced lipid accumulation and enhanced oxygen consumption and UCP1 protein expression, while inhibition of AMPK by dorsomorphin (5 µM) significantly reversed these effects. Conclusion: ALA improves estrogen deficiency-induced obesity via browning of WAT through AMPK signaling.

Hepatic danger signaling triggers TREM2+ macrophage induction and drives steatohepatitis via MS4A7-dependent inflammasome activation.

Metabolic dysfunction-associated steatohepatitis (MASH), formerly known as nonalcoholic steatohepatitis (NASH), is an advanced stage of metabolic fatty liver disease. The pathogenic mechanisms of MASH center on hepatocyte injury and the ensuing immune response within the liver microenvironment. Recent work has implicated TREM2+ macrophages in various disease conditions, and substantial induction of TREM2+ NASH-associated macrophages (NAMs) serves as a hallmark of metabolic liver disease. Despite this, the mechanisms through which NAMs contribute to MASH pathogenesis remain poorly understood. Here, we identify membrane-spanning 4-domains a7 (MS4A7) as a NAM-specific pathogenic factor that exacerbates MASH progression in mice. Hepatic MS4A7 expression was strongly induced in mouse and human MASH and associated with the severity of liver injury. Whole-body and myeloid-specific ablation of Ms4a7 alleviated diet-induced MASH pathologies in male mice. We demonstrate that exposure to lipid droplets (LDs), released upon injury of steatotic hepatocytes, triggered NAM induction and exacerbated MASH-associated liver injury in an MS4A7-dependent manner. Mechanistically, MS4A7 drove NLRP3 inflammasome activation via direct physical interaction and shaped disease-associated cell states within the liver microenvironment. This work reveals the LD-MS4A7-NLRP3 inflammasome axis as a pathogenic driver of MASH progression and provides insights into the role of TREM2+ macrophages in disease pathogenesis.

Quantitative analysis of the relationship between the myocardial bridge and the FAI of pericoronal fat on computed tomography.

We performed this cohort study to investigate whether the myocardial bridge (MB) affects the fat attenuation index (FAI) and to determine the optimal cardiac phase to measure the volume and the FAI of pericoronary adipose tissue (PCAT). The data of 300 patients who were diagnosed with MB of the left anterior descending (LAD) coronary artery were retrospectively analyzed. All of patients were divided into the MB group and the MB with atherosclerosis group. In addition, 104 patients with negative CCTA results were enrolled as the control group. There was no significant difference between FAI values measured in systole and diastole (P > 0.05). There was no significant difference in FAI among the MB group, the MB with atherosclerosis group, and the control group (P > 0.05). In MB with atherosclerosis group, LAD stenosis degree (< 50%) (OR = 0.186, 95% CI 0.036-0.960; P = 0.045) and MB located in the distal part of LAD opening (OR = 0.880, 95% CI 0.789-0.980; P = 0.020) were protective factors of FAI value. A distance (from the LAD opening to the proximal point of the MB) of 29.85 mm had the highest predictive value for abnormal FAI [area under the curve (AUC), 0.798], with a sensitivity of 81.1% and a specificity of 74.6%.

The kainate receptor GluK2 mediates cold sensing in mice.

Thermosensors expressed in peripheral somatosensory neurons sense a wide range of environmental temperatures. While thermosensors detecting cool, warm and hot temperatures have all been extensively characterized, little is known about those sensing cold temperatures. Though several candidate cold sensors have been proposed, none has been demonstrated to mediate cold sensing in somatosensory neurons in vivo, leaving a knowledge gap in thermosensation. Here we characterized mice lacking the kainate-type glutamate receptor GluK2, a mammalian homolog of the Caenorhabditis elegans cold sensor GLR-3. While GluK2 knockout mice respond normally to heat and mechanical stimuli, they exhibit a specific deficit in sensing cold but not cool temperatures. Further analysis supports a key role for GluK2 in sensing cold temperatures in somatosensory DRG neurons in the periphery. Our results reveal that GluK2-a glutamate-sensing chemoreceptor mediating synaptic transmission in the central nervous system-is co-opted as a cold-sensing thermoreceptor in the periphery.

Quantitative computed tomography angiography evaluation of the coronary fractional flow reserve in patients with left anterior descending artery myocardial bridging.

PURPOSE: To quantitatively investigate the effect of myocardial bridge (MB) in the left anterior descending artery (LAD) on the fractional flow reserve (FFR). MATERIALS AND METHODS: Three-hundred patients with LAD MB who had undergone coronary artery CT angiography (CCTA) were retrospectively enroled, and 104 normal patients were enroled as the control. The CCTA-derived fractional flow reserve (FFRCT) was measured at the LAD 10 mm proximal (FFR1) and 20-40 mm distal (FFR3) to the MB and at the MB location (FFR2). RESULTS: FFR2 and FFR3 of the MB (with BM only) and MBLA (with both MB and atherosclerosis) groups were significantly (p < 0.01) lower than those of the control. The FFR3 distal to the MB was significantly lower (p < 0.01) than that of the control. The FFRCT of the whole LAD in the MBLA group was significantly (p < 0.05) lower than that of the MB and control group (p < 0.05). MB length (OR 1.061) and MB muscle index (odds ratio or OR 1.007) were two risk factors for abnormal FFRCT, and MB length was a significant independent risk factor for abnormal FFRCT (OR = 1.077). LAD stenosis degree was a risk factor for abnormal FFRCT values (OR 3.301, 95% confidence interval [CI] 1.441-7.562, p = 0.005) and was also a significant independent risk factor (OR = 3.369, 95% CI: 1.392-8.152; p = 0.007) for abnormal FFRCT. CONCLUSION: MB significantly affects the FFRCT of distal coronary artery. For patients with MB without atherosclerosis, the MB length is a risk factor significantly affecting FFRCT, and for patients with MB accompanied by atherosclerosis, LAD stenotic severity is an independent risk factor for FFRCT.

Inhibitory effects of naringenin on estrogen deficiency-induced obesity via regulation of mitochondrial dynamics and AMPK activation associated with white adipose tissue browning.

AIMS: Post-ovariectomy (OVX) changes in hormones induce obesity and white adipose tissue (WAT) inflammation. Increased energy expenditure via WAT browning is a novel therapeutic strategy for treating obesity. Naringenin (NAR) reduces inflammation and lipogenesis in obesity and attenuates estrogen deficiency-associated metabolic disorders; however, its role in WAT browning remains unclear. MATERIALS AND METHODS: We investigated NAR ability to inhibit estrogen deficiency-associated obesity in vivo using a rat model and in vitro using 3T3-L1 adipocytes. KEY FINDINGS: NAR significantly decreased the body weight and WAT mass of rats. O2 consumption, CO2 production, and energy expenditure were significantly lower in the OVX group than in the sham group, but NAR treatment reversed these effects of OVX. NAR treatment markedly improved glucose intolerance and lipid profiles as well as leptin, adiponectin, and irisin levels. NAR upregulated markers of browning and mitochondrial biogenesis in inguinal WAT. Moreover, it enhanced markers of mitochondrial fusion and inhibited fission via activating the AMP-activated protein kinase pathway. Similar results were observed in 3T3-L1 adipocytes. Moreover, NAR-induced mitochondrial biogenesis and fusion were suppressed by dorsomorphin (an AMP-activated protein kinase inhibitor). SIGNIFICANCE: NAR alleviates obesity and metabolic dysfunction through the induction of WAT browning achieved via the modulation of AMP-activated protein kinase-regulated mitochondrial dynamics in WATs. NAR supplementation may therefore represent a potential intervention for preventing postmenopausal adipose tissue dysregulation.

The therapeutic potential of dietary intervention: based on the mechanism of a tryptophan derivative-indole propionic acid on metabolic disorders.

Tryptophan (TRP) contributes to individual immune homeostasis and good condition via three complex metabolism pathways (5-hydroxytryptamine (5-HT), kynurenine (KP), and gut microbiota pathway). Indole propionic acid (IPA), one of the TRP derivatives of the microbiota pathway, has raised more attention because of its impact on metabolic disorders. Here, we retrospect increasing evidence that TRP metabolites/IPA derived from its proteolysis impact host health and disease. IPA can activate the immune system through aryl hydrocarbon receptor (AHR) and/or Pregnane X receptor (PXR) as a vital mediator among diet-caused host and microbe cross-talk. Different levels of IPA in systemic circulation can predict the risk of NAFLD, T2DM, and CVD. IPA is suggested to alleviate cognitive impairment from oxidative damage, reduce gut inflammation, inhibit lipid accumulation and attenuate the symptoms of NAFLD, putatively enhance the intestinal epithelial barrier, and maintain intestinal homeostasis. Now, we provide a general description of the relationships between IPA and various physiological and pathological processes, which support an opportunity for diet intervention for metabolic diseases.

Five similar anthocyanidin molecules display distinct disruptive effects and mechanisms of action on Aß1-42 protofibril: A molecular dynamic simulation study.

Alzheimer's disease (AD) is associated with the deposition of amyloid-ß (Aß) fibrillary aggregates. Disaggregation of Aß fibrils is considered as one of the promising AD treatments. Recent experimental studies showed that anthocyanidins, one type of flavonoids abundant in fruits/vegetables, can disaggregate Aß fibrillary aggregates. However, their relative disruptive capacities and underlying mechanisms are largely unknown. Herein, we investigated the detailed interactions between five most common anthocyanidins (cyanidin, aurantinidin, peonidin, delphinidin, and pelargonidin) and Aß protofibril (an intermediate of Aß fibrillization) by performing microsecond molecular dynamic simulations. We found that all five anthocyanidins can destroy F4-L34-V36 hydrophobic core and K28-A42 salt bridge, leading to Aß protofibril destabilization. Aurantinidin exhibits the strongest damage to Aß protofibril (with the most severe disruption on K28-A42 salt bridges), followed by cyanidin (with the most destructive effect on F4-L34-V36 core). Detailed analyses reveal that the protofibril-destruction capacities of anthocyanidins are subtly modulated by the interplay of anthocyanidin-protofibril hydrogen bonding, hydrophobic, aromatic stacking interactions, which are dictated by the number or location of hydroxyl/methyl groups of anthocyanidins. These findings provide important mechanistic insights into Aß protofibril disaggregation by anthocyanidins, and suggest that aurantinidin/cyanidin may serve as promising starting-points for the development of new drug candidates against AD.

Prognostic value of CT-derived fractional flow reserve and fat attenuation index in patients with suspected coronary artery disease: a sex-disaggregated analyses.

BACKGROUND: There are sex differences in many risk factors associated with coronary artery disease (CAD). CT-derived fractional flow reserve (CT-FFR) and fat attenuation index (FAI) have been shown to independently predict cardiovascular events. We aimed to examine the impact of sex on the prognostic value of CT-FFR and FAI in suspected CAD patients, and to examine the incremental prognostic value of FAI over CT-FFR in both sex. METHODS: A total of 1334 consecutive suspected CAD subjects who underwent coronary computed tomographic angiography (CCTA) were retrospectively collected. We divided the patients into males and females and calculated CT-FFR and FAI data from CCTA images. Kaplan-Meier analysis was used to assess the risk of major adverse cardiovascular events (MACE) stratified by CT-FFR and FAI in both sex. Cox regression models were used to assess the incremental prognostic value of FAI by adding the variable to a model that included CT-FFR and clinical variables. RESULTS: During a median follow-up of 2.08 years, 212 patients had MACE. CT-FFR ≤ 0.80 was significantly associated with MACE in both sex. FAI value of left anterior descending artery (FAI[LAD]) and FAI value of left circumflex (FAI[LCX]) ≥ 70.1 were significantly associated with MACE in females. FAI[LCX] added incremental prognostic value over clinical and CT-FFR variables in females, with hazard ratio (HR) 3.230 (1.982-5.265, P = 0.000), Harrel's C 0.669 (P < 0.001), net reclassification improvement (NRI) 0.161 (0.073-0.260, P < 0.001), and integrated discrimination index (IDI) 0.036 (0.008-0.090, P = 0.010). FAI[LAD] did not enhance risk prediction in females (Harrel's C 0.643, P = 0.054; NRI 0.041, P = 0.189; IDI 0.005, P = 0.259). The decision curve analysis demonstrated that the model including FAI[LCX] resulted in the highest net benefit. CONCLUSIONS: In suspected CAD patients, the prognostic value of CT-FFR is not significantly biased by sex. The prognostic value of FAI[LAD] and FAI[LCX] were significantly associated with MACE in females, but not males. FAI[LCX], not FAI[LAD], added incremental prognostic value over CT-FFR and might enhance CT-FFR risk stratification in females.

SMG: self-supervised masked graph learning for cancer gene identification.

Cancer genomics is dedicated to elucidating the genes and pathways that contribute to cancer progression and development. Identifying cancer genes (CGs) associated with the initiation and progression of cancer is critical for characterization of molecular-level mechanism in cancer research. In recent years, the growing availability of high-throughput molecular data and advancements in deep learning technologies has enabled the modelling of complex interactions and topological information within genomic data. Nevertheless, because of the limited labelled data, pinpointing CGs from a multitude of potential mutations remains an exceptionally challenging task. To address this, we propose a novel deep learning framework, termed self-supervised masked graph learning (SMG), which comprises SMG reconstruction (pretext task) and task-specific fine-tuning (downstream task). In the pretext task, the nodes of multi-omic featured protein-protein interaction (PPI) networks are randomly substituted with a defined mask token. The PPI networks are then reconstructed using the graph neural network (GNN)-based autoencoder, which explores the node correlations in a self-prediction manner. In the downstream tasks, the pre-trained GNN encoder embeds the input networks into feature graphs, whereas a task-specific layer proceeds with the final prediction. To assess the performance of the proposed SMG method, benchmarking experiments are performed on three node-level tasks (identification of CGs, essential genes and healthy driver genes) and one graph-level task (identification of disease subnetwork) across eight PPI networks. Benchmarking experiments and performance comparison with existing state-of-the-art methods demonstrate the superiority of SMG on multi-omic feature engineering.

Integrated network analysis and metabolomics reveal the molecular mechanism of Yinchen Sini decoction in CCl4-induced acute liver injury.

Objective: Yinchen Sini decoction (YCSND), a traditional Chinese medicine (TCM) formula, plays a crucial role in the treatment of liver disease. However, the bioactive constituents and pharmacological mechanisms of action remain unclear. The present study aimed to reveal the molecular mechanism of YCSND in the treatment of acute liver injury (ALI) using integrated network analysis and metabolomics. Methods: Ultra-high-performance liquid chromatography coupled with Q-Exactive focus mass spectrum (UHPLC-QE-MS) was utilized to identify metabolites in YCSND, and high-performance liquid chromatography (HPLC) was applied to evaluate the quality of four botanical drugs in YCSND. Cell damage and ALI models in mice were established using CCl4. 1H-NMR metabolomics approach, along with histopathological observation using hematoxylin and eosin (H&E), biochemical measurements, and reverse transcription quantitative real-time PCR (RT-qPCR), was applied to evaluate the effect of YCSND on CCl4- induced ALI. Network analysis was conducted to predict the potential targets of YCSND in ALI. Result: Our results showed that 89 metabolites in YCSND were identified using UHPLC-QE-MS. YCSND protected against ALI by reducing the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), and malondialdehyde (MDA) contents and increasing those of superoxide dismutase (SOD), and glutathione (GSH) both in vivo and in vitro. The 1H-NMRmetabolic pattern revealed that YCSND reversed CCl4-induced metabolic abnormalities in the liver. Additionally, the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis identified five pathways related to liver injury, including the PI3K-AKT, MAPK, HIF-1, apoptosis, and TNF signaling pathways. Moreover, RT-qPCR showed YCSND regulated the inflammatory response (Tlr4, Il6, Tnfα, Nfκb1, Ptgs2, and Mmp9) and apoptosis (Bcl2, Caspase3, Bax, and Mapk3), and inhibited PI3K-AKT signaling pathway (Pi3k and Akt1). Combined network analysis and metabolomics showed a link between the key targets (Tlr4, Ptgs2, and Mmp9) and vital metabolites (choline, xanthine, lactate, and 3-hydroxybutyric acid) of YCSND in ALI. Conclusion: Overall, the results contribute to the understanding of the therapeutic effects of YCSND on ALI, and indicate that the integrated network analysis and metabolomics could be a powerful strategy to reveal the pharmacological effects of TCM.

Association of quantitative computed tomography-based right atrial appendage and right atrium parameters with postradiofrequency ablation recurrence of atrial fibrillation.

Background: The significance of the right atrial appendage (RAA) and right atrium (RA) in the recurrence of atrial fibrillation (AF) after radiofrequency ablation (RFA) remains uncertain. This retrospective case-control study aimed to quantitatively evaluate the role of morphological parameters of the RAA and RA in the recurrence of AF after RFA based on 256-slice spiral computed tomography (CT). Methods: A total of 297 patients with AF who underwent RFA for the first time between January 1 and October 31, 2020, were enrolled in the study, and they were divided into a nonrecurrence group (n=214) and a recurrence group (n=83). The volume of the RA, RAA and left atrium (LA); height of the RAA; long and short diameter, perimeter, and area of the RAA base; right atrial anteroposterior diameter; tricuspid annulus diameter; crista terminalis thickness; and cavotricuspid isthmus (CVTI) were measured, and the clinical data of patients were collected. Results: (I) Multivariable logistic regression analysis followed by univariable logistic regression analysis showed that the height of the RAA [odds ratio (OR) =1.124; 95% confidence interval (CI): 1.024-1.233; P=0.014], short diameter of the RAA base (OR =1.247; 95% CI: 1.118-1.391; P=0.001), crista terminalis thickness (OR =1.594; 95% CI: 1.052-2.415; P=0.028) and duration of AF (OR =1.009; 95% CI: 1.003-1.016; P=0.006) were independent predictors of postradiofrequency ablation AF recurrence. (II) Receiver operating characteristic (ROC) curve analysis showed that the prediction model constructed according to the multivariate logistic regression analysis presented good accuracy [area under the curve (AUC) =0.840; P=0.001]. A short diameter of the RAA base >26.95 mm had the highest predictive value for AF recurrence, with a sensitivity of 0.614 and a specificity of 0.822 (AUC =0.786, P=0.001). Pearson correlation analysis showed that there was a significant correlation between right atrial volume and left atrial volume (r=0.720, P<0.001). Conclusions: A significant increase in diameter and volume of the RAA and RA and tricuspid annulus diameter may correlate with postradiofrequency ablation AF recurrence. The height of the RAA, short diameter of the RAA base, crista terminalis thickness, and AF duration were independent predictors of recurrence. Among them, the short diameter of the RAA base had the highest predictive value for recurrence.

Modified stochastic medium prediction model for the deformation response of concealed underground stations under existing pipelines.

The underground pipeline network in the city is so intertwined that the concealed excavation of a metro station inevitably leads to a series of underground pipelines, causing settlement deformation and further risk of leakage. The existing theoretical methods for analysing settlement deformation are mostly for circular chambers, whereas metro stations have a nearly square cross-sectional form and different construction methods are very different, which have a greater impact on the deformation of the overlying pipelines. In this paper, based on the random medium theory and Peck's formula, the improved random medium model for predicting ground deformation is modified, the correction coefficients λ and η for the influence of different construction methods are proposed, the prediction model of underground pipeline deformation under different construction methods is obtained, and the numerical models of four work methods commonly used in urban tunnel construction: pillar hole method, side hole method, middle hole method and Pile-Beam-Arch (PBA) method are constructed through simulation, and the mathematical analysis software was used to fit the results to the model and obtain the range of correction coefficients λ and η for each of the four methods, and the accuracy and applicability of the theoretical model was verified by combining with actual engineering cases. The influence on the overlying pipes is in descending order: side hole method, pillar hole method, middle hole method and PBA method. The theoretical model provided in this paper for predicting the deformation of pipes in any overlying strata of the tunnel is well suited to the actual project and has a high degree of correlation with the measured results.