ObjectiveTo investigate the changes in chemical components of Gardeniae Fructus（GF） before and after being charred， providing data support for research on the material basis of GF Carbonisata（GFC）. MethodsUltra-performance liquid chromatography-quadrupole-electrostatic field orbitrap high-resolution mass spectrometry（UPLC-Q-Orbitrap MS/MS） was used to conduct a comprehensive analysis of the chemical components in GF and GFC under positive and negative ion modes with Compound Discoverer 3.3 software and online database. Then， principal component analysis and partial least squares-discriminant analysis in SIMCA14.1 software were used to analyze the MS data of each sample. Based on the principle of variable importance in the projection（VIP） value>1， differential secondary and primary metabolites before and after carbonization were screened. In addition， MetaboAnalyst website was used for pathway enrichment of Kyoto Encyclopedia of Genes and Genomes（KEGG）， so as to provide a reference for clarifying the processing mechanism. ResultsA total of 185 components were identified， including 96 secondary metabolites and 89 primary metabolites. These components were classified into nine categories， primarily including iridoid glycosides， flavonoids， and terpenoids， their fragmentation pathways were also analyzed. Simultaneously， multivariate statistical analysis was performed on the secondary and primary metabolites， identifying 70 and 59 differential metabolites， respectively. The secondary metabolites were enriched in two metabolic pathways， including C5-branched dibasic acid metabolism and flavonoid and flavonol biosynthesis， while the primary differential metabolites were enriched in seven pathways such as linoleic acid metabolism and tyrosine metabolism. ConclusionThe chemical components of GF change significantly after carbonization， with a significant decrease in the contents of iridoid glycosides and terpenoids such as hydroxyisogeniposide， crocin Ⅱ， crocetin， and jasminoside B. while the contents of 4-hydroxycoumarin， geniposidic acid， gentiopicroside， and gardenoside methyl ester increase significantly. This change is presumed to be associated with the enhanced cooling and hemostatic effects of the processed products. The identified key components provide a basis for elucidating the material basis underlying the efficacy changes before and after carbonization.

Objective To construct radiomics-semantic models to predict the treatment resistance of chemoradiotherapy in brain gliomas based on MRI and clinical data of multicenter patients.Methods Among 2 108 brain gliomas patients from five medical institutions,132 patients had residual gliomas after surgery.The clinical risk factors and multimodal MRI were collected.All patients were divided into training set(n=95)and validation set(n=37).The treatment response of gliomas after standardized chemoradiotherapy were divided into resistant and non-resistant types.The semantic features of MRI were evaluated by two radiologists.Three different segmentation regions of interest(ROI)were delineated to extract radiomics features.And that three groups of radiomics models were con-structed based on different sequence MRIs.The radiomics model with the best predictive efficacy in each group was selected and combined with MRI semantic features,three radiomics-semantic models(combined models)were established.Finally,a MRI semantic model,three groups of radiomics models and three combined models were developed.Results Comparisons between the different models showed that the radiomics-semantic model based on pre-operative T2-fluid attenuated inversion recovery(FLAIR)sequence,had the best predictive efficacy,the area under the curve(AUC)in the training and validation sets were 0.866[95％confidence interval(CI)0.790-0.942]and 0.810(95％CI 0.667-0.952),respectively.The radiomics-semantic model based on postoperative T1 WI sequence performed the second best,with the AUC of the training and validation sets being 0.812(95％CI 0.726-0.898)and 0.711(95％CI 0.541-0.881),respectively.Conclusion The combined models based on MRI radiomics and semantic features are able to predict the treatment resistance of chemoradiotherapy in brain gliomas patients,and may be used as an important basis for optimizing treatment.

Objective To construct radiomics-semantic models to predict the treatment resistance of chemoradiotherapy in brain gliomas based on MRI and clinical data of multicenter patients.Methods Among 2 108 brain gliomas patients from five medical institutions,132 patients had residual gliomas after surgery.The clinical risk factors and multimodal MRI were collected.All patients were divided into training set(n=95)and validation set(n=37).The treatment response of gliomas after standardized chemoradiotherapy were divided into resistant and non-resistant types.The semantic features of MRI were evaluated by two radiologists.Three different segmentation regions of interest(ROI)were delineated to extract radiomics features.And that three groups of radiomics models were con-structed based on different sequence MRIs.The radiomics model with the best predictive efficacy in each group was selected and combined with MRI semantic features,three radiomics-semantic models(combined models)were established.Finally,a MRI semantic model,three groups of radiomics models and three combined models were developed.Results Comparisons between the different models showed that the radiomics-semantic model based on pre-operative T2-fluid attenuated inversion recovery(FLAIR)sequence,had the best predictive efficacy,the area under the curve(AUC)in the training and validation sets were 0.866[95％confidence interval(CI)0.790-0.942]and 0.810(95％CI 0.667-0.952),respectively.The radiomics-semantic model based on postoperative T1 WI sequence performed the second best,with the AUC of the training and validation sets being 0.812(95％CI 0.726-0.898)and 0.711(95％CI 0.541-0.881),respectively.Conclusion The combined models based on MRI radiomics and semantic features are able to predict the treatment resistance of chemoradiotherapy in brain gliomas patients,and may be used as an important basis for optimizing treatment.

Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin regions, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at the single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences on TF binding. Notably, cFOOT-seq, combined with FootTrack analysis, enables de novo prediction of TF binding sites and tracking of TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.
Transcription Factors/genetics* ; Humans ; Chromatin/genetics* ; Animals ; Binding Sites ; Mice ; DNA Footprinting/methods*

Chinese medicinal materials serve as the material foundation of traditional Chinese medicine （TCM） culture. The sustainable development of Chinese medicinal material resources is a focal point in the modernization of TCM. With the increasing scarcity of Chinese medicinal material resources， the expansion of new Chinese medicinal material resources has become a crucial means for the sustainable utilization of these resources. New Chinese medicinal material resources refer to natural resources that have been newly discovered or developed， possessing potential medicinal value or healthcare functions， which fall outside the traditional application scope of herbal medicines. These resources have not yet been widely recognized or applied within the framework of traditional TCM theory. They specifically include artificial substitutes for endangered medicinal materials， new medicinal parts of medicinal plants， medicinal materials with expanded clinical applications， and foreign medicinal resources. The rational compatability and formulation of new Chinese medicinal material resources are essential pathways for integrating them into the TCM system. Due to the weak foundational research on new Chinese medicinal material resources in China， the characteristics of these resources that align with the TCM theory are not yet fully understood， posing numerous constraints on formulating prescriptions based on the traditional compatibility principles of TCM. This paper integrates the traditional formulation theory of TCM with modern data integration methods， proposing four formulation models for new TCM resources： synergistic compatibility， substitutive compatibility， symptom-based compatibility， and efficacy semantic compatibility. These models provide new insights for the application of new Chinese medicinal material resources， not only facilitating their rational use in clinical practice but also offering theoretical support for the development and compatibility research of these resources.

Chinese medicinal materials serve as the material foundation of traditional Chinese medicine （TCM） culture. The sustainable development of Chinese medicinal material resources is a focal point in the modernization of TCM. With the increasing scarcity of Chinese medicinal material resources， the expansion of new Chinese medicinal material resources has become a crucial means for the sustainable utilization of these resources. New Chinese medicinal material resources refer to natural resources that have been newly discovered or developed， possessing potential medicinal value or healthcare functions， which fall outside the traditional application scope of herbal medicines. These resources have not yet been widely recognized or applied within the framework of traditional TCM theory. They specifically include artificial substitutes for endangered medicinal materials， new medicinal parts of medicinal plants， medicinal materials with expanded clinical applications， and foreign medicinal resources. The rational compatability and formulation of new Chinese medicinal material resources are essential pathways for integrating them into the TCM system. Due to the weak foundational research on new Chinese medicinal material resources in China， the characteristics of these resources that align with the TCM theory are not yet fully understood， posing numerous constraints on formulating prescriptions based on the traditional compatibility principles of TCM. This paper integrates the traditional formulation theory of TCM with modern data integration methods， proposing four formulation models for new TCM resources： synergistic compatibility， substitutive compatibility， symptom-based compatibility， and efficacy semantic compatibility. These models provide new insights for the application of new Chinese medicinal material resources， not only facilitating their rational use in clinical practice but also offering theoretical support for the development and compatibility research of these resources.

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A strategy combining a tailored database and high-throughput activity screening that discover bioactive metabolites derived from Magnoliae Officinalis Cortex (MOC) was developed and implemented to rapidly profile and discover bioactive metabolites in vivo derived from traditional Chinese medicine (TCM). The strategy possessed four characteristics: 1) The tailored database consisted of metabolites derived from big data-originated reference compound, metabolites predicted in silico, and MOC chemical profile-based pseudomolecular ions. 2) When profiling MOC-derived metabolites in vivo, attentions were paid not only to prototypes of MOC compounds and metabolites directly derived from MOC compounds, as reported by most papers, but also to isomerized metabolites and the degradation products of MOC compounds as well as their derived metabolites. 3) Metabolite traceability was performed, especially to distinguish isomeric prototypes-derived metabolites, prototypes of MOC compounds as well as phase I metabolites derived from other MOC compounds. 4) Molecular docking was utilized for high-throughput activity screening and molecular dynamic simulation as well as zebrafish model were used for verification. Using this strategy, 134 metabolites were swiftly characterized after the oral administration of MOC to rats, and several metabolites were reported for the first time. Furthermore, 17 potential active metabolites were discovered by targeting the motilin, dopamine D2, and the serotonin type 4 (5-HT₄) receptors, and part bioactivities were verified using molecular dynamic simulation and a zebrafish constipation model. This study extends the application of mass spectrometry (MS) to rapidly profile TCM-derived metabolites in vivo, which will help pharmacologists rapidly discover potent metabolites from a complex matrix.

Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder affecting a substantial proportion of women of reproductive age. It is frequently associated with ovulatory dysfunction, infertility, and an increased risk of chronic metabolic diseases. A hallmark pathological feature of PCOS is the arrest of follicular development, closely linked to impaired intercellular communication between the oocyte and surrounding granulosa cells. Transzonal projections (TZPs) are specialized cytoplasmic extensions derived from granulosa cells that penetrate the zona pellucida to establish direct contact with the oocyte. These structures serve as essential conduits for the transfer of metabolites, signaling molecules (e.g., cAMP, cGMP), and regulatory factors (e.g., microRNAs, growth differentiation factors), thereby maintaining meiotic arrest, facilitating metabolic cooperation, and supporting gene expression regulation in the oocyte. The proper formation and maintenance of TZPs depend on the cytoskeletal integrity of granulosa cells and the regulated expression of key connexins, particularly CX37 and CX43. Recent studies have revealed that in PCOS, TZPs exhibit significant structural and functional abnormalities. Contributing factors—such as hyperandrogenism, insulin resistance, oxidative stress, chronic inflammation, and dysregulation of critical signaling pathways (including PI3K/Akt, Wnt/β‑catenin, and MAPK/ERK)—collectively impair TZP integrity and reduce their formation. This disruption in granulosa-oocyte communication compromises oocyte quality and contributes to follicular arrest and anovulation. This review provides a comprehensive overview of TZP biology, including their formation mechanisms, molecular composition, and stage-specific dynamics during folliculogenesis. We highlight the pathological alterations in TZPs observed in PCOS and elucidate how endocrine and metabolic disturbances—particularly androgen excess and hyperinsulinemia—downregulate CX43 expression and impair gap junction function, thereby exacerbating ovarian microenvironmental dysfunction. Furthermore, we explore emerging therapeutic strategies aimed at preserving or restoring TZP integrity. Anti-androgen therapies (e.g., spironolactone, flutamide), insulin sensitizers (e.g., metformin), and GLP-1 receptor agonists (e.g., liraglutide) have shown potential in modulating connexin expression and enhancing granulosa-oocyte communication. In addition, agents such as melatonin, AMPK activators, and GDF9/BMP15 analogs may promote TZP formation and improve oocyte competence. Advanced technologies, including ovarian organoid models and CRISPR-based gene editing, offer promising platforms for studying TZP regulation and developing targeted interventions. In summary, TZPs are indispensable for maintaining follicular homeostasis, and their disruption plays a pivotal role in the pathogenesis of PCOS-related folliculogenesis failure. Targeting TZP integrity represents a promising therapeutic avenue in PCOS management and warrants further mechanistic and translational investigation.

ObjectiveThe U6 promoter is an essential element for driving sgRNA expression in the clustered regularly interspaced short palindromic repeat sequences/CRISPR-associated protein 9（CRISPR/Cas9）gene editing system in dicotyledonous plants. Endogenous U6 promoters typically exhibit higher transcriptional activity， which can significantly improve gene editing efficiency. This study aims to identify endogenous U6 promoters in Artemisia annua to optimize its CRISPR/Cas9 gene editing system， which holds significant importance for its molecular breeding. MethodsOn the basis of the highly conserved U6 snRNA sequences in Arabidopsis thaliana， endogenous U6 promoters were screened in the A. annua genome. Expression vectors were constructed with candidate AaU6 promoter driving the firefly luciferase （LUC） reporter gene， and then transiently transformed into Nicotiana benthamiana. Transcriptional activities of the promoters were measured and compared by in vivo imaging and the Dual Luciferase Reporter assay. ResultsEight endogenous U6 promoters were successfully cloned from A. annua. Sequences alignment revealed that all these promoters contained the two conserved cis-acting elements， upstream sequence element （USE） and TATA-box， which affected their transcriptional activity. Dual-luciferase activity assays indicated that the transcriptional activities of AaU6-3， AaU6-1， and AaU6-5 were significantly higher than that of the Arabidopsis AtU6-26 promoter， with AaU6-3 exhibiting the highest activity. ConclusionThis study identified three endogenous AaU6 promoters with high transcriptional activity in A. annua， providing key functional elements for establishing an efficient gene editing system in A. annua. These findings will contribute to advancing precision molecular breeding and high-quality germplasm innovation in A. annua.