ObjectiveTransfer RNA-derived fragments (tRFs) are a recently characterized and rapidly expanding class of small non-coding RNAs, typically ranging from 13 to 50 nucleotides in length. They are derived from mature or precursor tRNA molecules through specific cleavage events and have been implicated in a wide range of cellular processes. Increasing evidence indicates that tRFs play important regulatory roles in gene expression, primarily by interacting with target messenger RNAs (mRNAs) to induce transcript degradation, in a manner partially analogous to microRNAs (miRNAs). However, despite their emerging biological relevance and potential roles in disease mechanisms, there remains a significant lack of computational tools capable of systematically predicting the interaction landscape between tRFs and their target mRNAs. Existing databases often rely on limited interaction features and lack the flexibility to accommodate novel or user-defined tRF sequences. The primary goal of this study was to develop a machine learning based prediction algorithm that enables high-throughput, accurate identification of tRF:mRNA binding events, thereby facilitating the functional analysis of tRF regulatory networks. MethodsWe began by assembling a manually curated dataset of 38 687 experimentally verified tRF:mRNA interaction pairs and extracting seven biologically informed features for each pair: (1) AU content of the binding site, (2) site pairing status, (3) binding region location, (4) number of binding sites per mRNA, (5) length of the longest consecutive complementary stretch, (6) total binding region length, and (7) seed sequence complementarity. Using this dataset and feature set, we trained 4 distinct machine learning classifiers—logistic regression, random forest, decision tree, and a multilayer perceptron (MLP)—to compare their ability to discriminate true interactions from non-interactions. Each model’s performance was evaluated using overall accuracy, receiver operating characteristic (ROC) curves, and the corresponding area under the ROC curve (AUC). The MLP consistently achieved the highest AUC among the four, and was therefore selected as the backbone of our prediction framework, which we named tRF Prospect. For biological validation, we retrieved 3 high-throughput RNA-seq datasets from the gene expression omnibus (GEO) in which individual tRFs were overexpressed: AS-tDR-007333 (GSE184690), tRF-3004b (GSE197091), and tRF-20-S998LO9D (GSE208381). Differential expression analysis of each dataset identified genes downregulated upon tRF overexpression, which we designated as putative targets. We then compared the predictions generated by tRF Prospect against those from three established tools—tRFTar, tRForest, and tRFTarget—by quantifying the number of predicted targets for each tRF and assessing concordance with the experimentally derived gene sets. ResultsThe proposed algorithm achieved high predictive accuracy, with an AUC of 0.934. Functional validation was conducted using transcriptome-wide RNA-seq datasets from cells overexpressing specific tRFs, confirming the model’s ability to accurately predict biologically relevant downregulation of mRNA targets. When benchmarked against established tools such as tRFTar, tRForest, and tRFTarget, tRF Prospect consistently demonstrated superior performance, both in terms of predictive precision and sensitivity, as well as in identifying a higher number of true-positive interactions. Moreover, unlike static databases that are limited to precomputed results, tRF Prospect supports real-time prediction for any user-defined tRF sequence, enhancing its applicability in exploratory and hypothesis-driven research. ConclusionThis study introduces tRF Prospect as a powerful and flexible computational tool for investigating tRF:mRNA interactions. By leveraging the predictive strength of deep learning and incorporating a broad spectrum of interaction-relevant features, it addresses key limitations of existing platforms. Specifically, tRF Prospect: (1) expands the range of detectable tRF and target types; (2) improves prediction accuracy through multilayer perceptron model; and (3) allows for dynamic, user-driven analysis beyond database constraints. Although the current version emphasizes miRNA-like repression mechanisms and faces challenges in accurately capturing 5'UTR-associated binding events, it nonetheless provides a critical foundation for future studies aiming to unravel the complex roles of tRFs in gene regulation, cellular function, and disease pathogenesis.

Emodin is a hydroxyanthraquinone compound that is widely distributed and has multiple pharmacological activities, including anti-diarrheal, anti-inflammatory, and liver-protective effects. Research indicates that emodin may be one of the main components responsible for inducing hepatotoxicity. However, studies on the mechanisms of liver injury are relatively limited, particularly those related to bile acids(BAs) metabolism. This study aims to systematically investigate the effects of different dosages of emodin on BAs metabolism, providing a basis for the safe clinical use of traditional Chinese medicine(TCM)containing emodin. First, this study evaluated the safety of repeated administration of different dosages of emodin over a 5-week period, with a particular focus on its impact on the liver. Next, the composition and content of BAs in serum and liver were analyzed. Subsequently, qRT-PCR was used to detect the mRNA expression of nuclear receptors and transporters related to BAs metabolism. The results showed that 1 g·kg~(-1) emodin induced hepatic damage, with bile duct hyperplasia as the primary pathological manifestation. It significantly increased the levels of various BAs in the serum and primary BAs(including taurine-conjugated and free BAs) in the liver. Additionally, it downregulated the mRNA expression of farnesoid X receptor(FXR), retinoid X receptor(RXR), and sodium taurocholate cotransporting polypeptide(NTCP), and upregulated the mRNA expression of cholesterol 7α-hydroxylase(CYP7A1) in the liver. Although 0.01 g·kg~(-1) and 0.03 g·kg~(-1) emodin did not induce obvious liver injury, they significantly increased the level of taurine-conjugated BAs in the liver, suggesting a potential interference with BAs homeostasis. In conclusion, 1 g·kg~(-1) emodin may promote the production of primary BAs in the liver by affecting the FXR-RXR-CYP7A1 pathway, inhibit NTCP expression, and reduce BA reabsorption in the liver, resulting in BA accumulation in the peripheral blood. This disruption of BA homeostasis leads to liver injury. Even doses of emodin close to the clinical dose can also have a certain effect on the homeostasis of BAs. Therefore, when using traditional Chinese medicine or formulas containing emodin in clinical practice, it is necessary to regularly monitor liver function indicators and closely monitor the risk of drug-induced liver injury.
Emodin/administration & dosage* ; Bile Acids and Salts/metabolism* ; Animals ; Male ; Liver/injuries* ; Chemical and Drug Induced Liver Injury/genetics* ; Drugs, Chinese Herbal/adverse effects* ; Humans ; Rats, Sprague-Dawley ; Mice ; Rats

OBJECTIVES: To investigate the role and mechanism of copper overload-mediated endoplasmic reticulum stress (ERS) in vascular endothelial injury in Kawasaki disease (KD). METHODS: Four-week-old male C57BL/6 mice were randomly divided into four groups: control, KD, KD plus copper chelator tetrathiomolybdate (TTM), and KD plus ERS inhibitor AMG PERK 44 (AMG) (n=20 per group). A KD mouse model was established using Candida albicans extract. Human umbilical vein endothelial cells (HUVECs) were divided into control (intervention with healthy children's serum), KD (intervention with KD patients' serum), and KD+TTM (intervention with KD patients' serum plus 20 µmol/L TTM). Copper deposition in mouse heart tissue was assessed using rubeanic acid staining. Vascular pathological changes were observed using hematoxylin-eosin staining and measurement of abdominal aortic diameter and area. ERS activation was detected by transmission electron microscopy and immunofluorescence. HUVEC viability, apoptosis, and functional changes were evaluated using CCK8, flow cytometry, cell scratch assay, and angiogenesis experiments. ERS marker protein expression levels were measured by Western blot. RESULTS: Compared to the KD group, the KD+TTM and KD+AMG groups showed reduced copper deposition in the vascular wall, decreased swelling of coronary endothelial cells and endoplasmic reticulum, reduced inflammatory cell infiltration, and less abdominal aortic lesion expansion. The abdominal aortic diameter and area, and the fluorescence intensity of ERS marker proteins (GRP78 and CHOP) were significantly lower (P<0.05). Compared to the KD group, the KD+TTM group exhibited increased cell viability, tube number, and scratch healing rate, along with decreased apoptosis rate and expression of ERS marker proteins (GRP78, CHOP, ATF6, and p-PERK) (P<0.05). CONCLUSIONS Copper overload aggravates vascular endothelial injury in KD by activating the ERS pathway. TTM can exert protective effects on the endothelium by regulating copper metabolism and inhibiting the ERS pathway.
Endoplasmic Reticulum Stress ; Copper/toxicity* ; Male ; Mucocutaneous Lymph Node Syndrome/metabolism* ; Animals ; Humans ; Endoplasmic Reticulum Chaperone BiP ; Mice, Inbred C57BL ; Mice ; Human Umbilical Vein Endothelial Cells ; Apoptosis ; Endothelium, Vascular/injuries*

BACKGROUND: Non-invasive computed tomography angiography (CTA)-based fractional flow reserve (CT-FFR) could become a gatekeeper to invasive coronary angiography. Deep learning (DL)-based CT-FFR has shown promise when compared to invasive FFR. To evaluate the performance of a DL-based CT-FFR technique, DeepVessel FFR (DVFFR). METHODS: This retrospective study was designed for iScheMia Assessment based on a Retrospective, single-center Trial of CT-FFR (SMART). Patients suspected of stable coronary artery disease (CAD) and undergoing both CTA and invasive FFR examinations were consecutively selected from the Beijing Anzhen Hospital between January 1, 2016 to December 30, 2018. FFR obtained during invasive coronary angiography was used as the reference standard. DVFFR was calculated blindly using a DL-based CT-FFR approach that utilized the complete tree structure of the coronary arteries. RESULTS: Three hundred and thirty nine patients (60.5 ±10.0 years and 209 men) and 414 vessels with direct invasive FFR were included in the analysis. At per-vessel level, sensitivity, specificity, accuracy, positive predictive value (PPV) and negative predictive value (NPV) of DVFFR were 94.7%, 88.6%, 90.8%, 82.7%, and 96.7%, respectively. The area under the receiver operating characteristics curve (AUC) was 0.95 for DVFFR and 0.56 for CTA-based assessment with a significant difference (P < 0.0001). At patient level, sensitivity, specificity, accuracy, PPV and NPV of DVFFR were 93.8%, 88.0%, 90.3%, 83.0%, and 95.8%, respectively. The computation for DVFFR was fast with the average time of 22.5 ± 1.9 s. CONCLUSIONS The results demonstrate that DVFFR was able to evaluate lesion hemodynamic significance accurately and effectively with improved diagnostic performance over CTA alone. Coronary artery disease (CAD) is a critical disease in which coronary artery luminal narrowing may result in myocardial ischemia. Early and effective assessment of myocardial ischemia is essential for optimal treatment planning so as to improve the quality of life and reduce medical costs.

Hearing loss is the most prevalent disabling disease. Cochlear implantation（CI） serves as the primary intervention for severe to profound hearing loss. This consensus systematically explores the value of genetic diagnosis in the pre-operative assessment and efficacy prognosis for CI. Drawing upon domestic and international research and clinical experience, it proposes an evidence-based medicine three-tiered prognostic classification system（Favorable, Marginal, Poor）. The consensus focuses on common hereditary non-syndromic hearing loss（such as that caused by mutations in genes like GJB2, SLC26A4, OTOF, LOXHD1） and syndromic hereditary hearing loss（such as Jervell & Lange-Nielsen syndrome and Waardenburg syndrome）, which are closely associated with congenital hearing loss, analyzing the impact of their pathological mechanisms on CI outcomes. The consensus provides recommendations based on multiple round of expert discussion and voting. It emphasizes that genetic diagnosis can optimize patient selection, predict prognosis, guide post-operative rehabilitation, offer stratified management strategies for patients with different genotypes, and advance the application of precision medicine in the field of CI.
Humans ; Cochlear Implantation ; Prognosis ; Hearing Loss/surgery* ; Consensus ; Connexin 26 ; Mutation ; Sulfate Transporters ; Connexins/genetics*

In-depth study of the components of polymyxins is the key to controlling the quality of this class of antibiotics. Similarities and variations of components present significant analytical challenges. A two-dimensional (2D) liquid chromatography-mass spectrometr (LC-MS) method was established for screening and comprehensive profiling of compositions of the antibiotic colistimethate sodium (CMS). A high concentration of phosphate buffer mobile phase was used in the first-dimensional LC system to get the components well separated. For efficient and high-accuracy screening of CMS, a targeted method based on a self-constructed high resolution (HR) mass spectrum database of CMS components was established. The database was built based on the commercial MassHunter Personal Compound Database and Library (PCDL) software and its accuracy of the compound matching result was verified with six known components before being applied to genuine sample screening. On this basis, the unknown peaks in the CMS chromatograms were deduced and assigned. The molecular formula, group composition, and origins of a total of 99 compounds, of which the combined area percentage accounted for more than 95% of CMS components, were deduced by this 2D-LC-MS method combined with the MassHunter PCDL. This profiling method was highly efficient and could distinguish hundreds of components within 3 h, providing reliable results for quality control of this kind of complex drugs.

Objective To evaluate the bioequivalence and safety of ibuprofen arginine granules test and reference formulations in Chinese healthy volunteers under fasting and postprandial conditions,and to provide evidence for consistency evaluation and clinical application of the drugs.Methods A single-center,single-dose,randomized,open-label,fasting and postprandial,two-period,two-crossover trial design was used.Twenty-four healthy Chinese volunteers were enrolled in the fasting and postprandial trial,respectively.The test preparation and reference preparation of ibuprofen arginine granules 0.4 g were taken orally in a randomized crossover single dose.Data analysis was performed using Phoenix WinNonlin 8.3.Results In the fasting group,the main pharmacokinetic parameters of ibuprofen in plasma after administration of the test and reference formulations of ibuprofen arginine granules were as follows:Cmax were(51.07±7.43)and(50.10±7.64)μg·mL-1;AUC0-,were(122.78±20.62)and(119.94±21.03)μg·h·mL-1;AUC0_∞ were(125.84±21.31)and(122.64±21.87)μg·h·mL-1,respectively.In the postprandial group,the main pharmacokinetic parameters of ibuprofen in plasma after administration of the test and reference formulations of ibuprofen arginine granules were as follows:Cmax were(17.47±3.56)and(17.89±4.47)μg·mL-1;AUC0-twere(114.33±17.12)and(122.13±29.46)μg·h·mL-1;AUC0_∞ were(134.04±36.72)and(133.96±30.35)μg·h·mL-1,respectively.The 90％confidence intervals of the geometric mean ratio of the two preparations were as follows:Cmax 97.96％-106.02％,AUC0_t 98.77％-105.14％,AUC0-∞ 99.34％-105.19％in fasting group;in postprandial group,Cmax was 92.37％-103.05％,AUC0-t was 93.31％-99.56％,AUC0-∞ was 93.89％-102.91％.Conclusion The test preparation and reference preparation of ibuprofen arginine granules in this study are bioequivalent in healthy adult Chinese volunteers.

Objective The contents of 11 nucleosides and base components in 10 batches of samples from 5 provinces(cities)including Chongqing,Yunnan and Shaanxi were determined,and the differences in nucleosides and base components in Fritillaria taipaiensis were compared by chemometric analysis,and the quality was comprehensively evaluated,so as to provide a reference for the cultivation of excellent varieties and the selection of medicinal materials.Methods Nucleoside and base components were extracted from Fritillaria taipaiensis by ultrasonication in aqueous solutions,and the content of each component was determined by HPLC-DAD method.The origin was classified by principal component analysis(PCA)and hierarchical cluster analysis(HCA).Partial least squares discriminant analysis(PLS-DA)was used to determine the differentiated index components in Fritillaria taipaiensis.Then the differences in the contents of the index components among samples from different origins were compared.Results It was found that 11 nucleoside and base components differed significantly among different origins of Fritillaria taipaiensis.Principal component analysis and hierarchical cluster analysis indicated that all samples could be clustered into 4 categories.Five characteristic components,including uracil,cytosine,uridine,inosine,and adenosine,were identified by PLS-DA.The nucleosides and bases in samples from Chongqing and Hubei were relatively high,and the quality of the samples was comparatively superior.Conclusion This method is simple,reproducible,accurate and reliable.It has screened out the index nucleoside and base components in the identification of Fritillaria taipaiensis of different origins,which can be used to initially elucidate the differences of samples between different origins.Additionally,it can better reflect the quality of Fritillaria taipaiensis,and can provide reference for the selection of procurement origin and the quality control for Fritillaria taipaiensis.

Sishen Pills is a classic prescription for the treatment of spleen and kidney diarrhea,which has the effect of warming the kidney and the spleen,astringent intestine and antidiarrheal.In modern clinical application,the modified prescriptions based on Sishen Pills,combined with other treatments of TCM and integrated traditional Chinese and Western medicine are often used to treat ulcerative colitis with spleen-kidney yang deficiency syndrome,and the curative effect is remarkable.Experimental pharmacological studies have shown that Sishen Pills may achieve the purpose of ulcerative colitis by regulating the expression of related signaling pathway proteins,regulating inflammatory factors,inhibiting inflammatory response,regulating autophagy,regulating intestinal flora,improving intestinal mucosal permeability,repairing intestinal mucosal barrier,regulating cellular energy metabolism,anti-oxidative stress,regulating cellular immune function,etc.In this article,the research status of Sishen Pills in the treatment of ulcerative colitis was sorted out and summarized,in order to provide reference for further study of its mechanism and clinical application.

Objective To observe the inter-observer consistency of diameter of inferior vena cava(IVC)and IVC collapsibility index(IVCCI)measured and assessed with echocardiography and the correlations with right heart parameters in patients with right heart dysfunction.Methods Forty-seven patients with right heart dysfunction were prospectively recruited in observation group,while 50 adults with normal right heart function were taken as controls(control group).Parameters of the right heart were obtained with echocardiography,including the right ventricular fractional area change(FAC),the tricuspid annular plane systolic excursion(TAPSE),the myocardial performance index(MPI),the tricuspid annular systolic velocity(S')as well as early and late diastolic velocity(e',a')and e'/a' ratio,also the tricuspid valve orifice early and late diastolic velocities(E,A)and E/A ratio and E/e',the vena contracta width of tricuspid regurgitation(TR-VCW),the maximum velocity of tricuspid regurgitation(TR-Vmax),the pulmonary artery systolic pressure(PASP)and right atrial area(RAA).Besides,the maximal and minimal diameter of IVC(IVCDmax,IVCDmin)during the respiratory cycle were measured with two dimensional(2D)ultrasound and anatomical M-mode ultrasound,respectively,and the IVCCI were calculated.Then 20 subjects were randomly selected from each group,and IVC parameters were obtained.The basic data,right heart parameters and IVC parameters were compared between groups,intra-class correlation coefficient(ICC)between 2 sonographers of IVC parameters were calculated,and correlations between IVC parameters and right heart parameters were assessed.Results No significant differences of gender,age nor body mass index(BMI)was detected between groups(all P＞0.05).Compared with those in control group,MPI,e',e'/a',E,A,E/e',TR-VCW,TR-Vmax,PASP and RAA increased,whereas FAC,TAPSE,S'and a'decreased in observation group(all P＜0.05).The inter-observer consistencies were good for IVCDmax and IVCCI in observation group(ICC=0.787-0.971)and IVCDmax in the control group(ICC=0.971,0.964)obtained with 2D ultrasound and anatomical M-mode ultrasound,but poor for IVCCI in control group(ICC=0.169,0.456).Compared with those in control group,IVC parameters 2D-IVCDmax,2D-IVCDmin,M-IVCDmax and M-IVCDmin increased but 2D-IVCCI and M-IVCCI decreased in observation group(all P＜0.05).In control group,2D-IVCDmax was weakly negatively correlated with TAPSE and a'(r=-0.392,-0.364),weakly positively correlated with e'/a',E,E/A,TR-VCW and RAA(r=0.396,0.483,0.461,0.565,0.582),2D-IVCCI was weakly negatively correlated with TR-VCW and RAA(r=-0.386,-0.380),while M-IVCDmax was weakly negatively correlated with TAPSE(r=-0.384),and weakly positively correlated with e'/a',E,E/A,TR-VCW and RAA(r=0.357,0.453,0.473,0.549,0.550),M-IVCCI was weakly negatively correlated with MPI,E,TR-VCW and RAA(r=-0.347,-0.337,-0.475,-0.421).Conclusion In patients with right heart dysfunction,IVCD diameter and IVCCI obtained with echocardiography had good inter-observer consistencies.Parameters obtained with 2D ultrasound and anatomic M-mode ultrasound had certain relations with the right heart parameters.