1.Performance verification and results analysis of DNA workflow for metagenomic next-generation sequencing
Shangdong YANG ; Yang XIAO ; Wen XI ; Zhe LIU ; Fang WANG ; Xiaoqin WANG
Journal of Xi'an Jiaotong University(Medical Sciences) 2025;46(1):162-168
Objective To establish a performance verification scheme for the metagenomic next-generation sequencing(mNGS)DNA workflow.Methods Reference materials and clinical samples were used for conducting experiments.The mNGS detection results were evaluated in terms of limit of detection(LOD),repeatability,robustness,anti-interference ability,specificity and accuracy,as well as the patterns of library construction and the performance of sequencers.Results All species in the reference materials were stably detected,and the LOD of mNGS was 5.0E+02 CFU/mL(copies/mL).The repeatability was 100%and the within-batch(coefficient of variation)CV ranged from 8.53%to 38.73%.The linear correlation coefficient|r|>0.9 was found between the input pathogenic microorganism concentration and the read count.Meanwhile,the experimental robustness was found to be good.The results of the anti-interference test showed that the higher concentration of human DNA inputted,the fewer pathogenic microorganism read counts detected by mNGS.Meanwhile,the read counts of related species presented a proportional relationship with the corresponding pathogenic microorganisms concentration inputted,which meant the validation of the cross-interference test had been passed.Furthermore,the detection result of D0 was negative.The accuracy of clinical samples testing was 90.9%(10/11).In addition,the library quality control results obtained by the automatic liquid handling workstation and manually operation were all acceptable.The performance of the three Illumina sequencers met or were better than the factory standards.Conclusion The clinical laboratory performance verification scheme for mNGS detection was established,which included the design for reference materials,comparison of different patterns for library construction,and performance evaluation of the sequencers.More importantly,the performance verification scheme can be used to evaluate and ensure the quality of mNGS DNA workflow detection process.
2.Atomic force microscopic observation of surface structure of purified protein molecules in vitro
Zhao-ying CHEN ; Xiao-feng FANG ; Dan-yan LIU ; Meng-qin CHEN ; Xi LING ; Jie-min ZHAO ; Wei WEI ; Yu-jing WU
Chinese Pharmacological Bulletin 2025;41(1):193-199
Aim To compare the observation results of atomic force microscopy(AFM)and scanning electron microscopy(SEM),and to summarize the main problems and solutions of AFM in observing biological macromolecules,using the observa-tion subjects of protein samples purified by our research group.Methods The protein samples were diluted to 15 nmol·L-1 with PBS,fixed on glass slides,silicon wafers,and mica sheets,dried,and made into solid-phase observation samples.SEM sam-ples were plated with platinum before observation.The surface structures of proteins were observed using AFM and SEM,sample heights were calculated,and differences in results were com-pared.Results Protein samples with positive charges tended to shift to the right during observation due to the repulsion of the AFM probe;mica sheets could effectively eliminate the positive charge of proteins to avoid sample movement;PBS provided a stable environment for protein samples,but the crystallization of PBS salts interfered with probe operation and imaging clarity;SEM samples needed to be plated with platinum before observa-tion and could not achieve the precision of AFM.Conclusions Both AFM and SEM can directly observe protein structures in vitro,with AFM providing higher precision results;when protein sample stability permits,ultrapure water is preferred as the sol-vent carrier,and volatile liquids such as ethanol can also serve as solvent carriers.The application of AFM offers a new approach for pharmacological studies on interactions between biological macromolecules.
3.Guideline for diagnosis and treatment of infection after internal fixation of closed lower limb fractures in adults (version 2025)
Bobin MI ; Faqi CAO ; Weixian HU ; Wu ZHOU ; Chenchen YAN ; Hui LI ; Yun SUN ; Yuan XIONG ; Jinmi ZHAO ; Qikai HUA ; Xinbao WU ; Xieyuan JIANG ; Dianying ZHANG ; Zhongguo FU ; Dankai WU ; Guangyao LIU ; Guodong LIU ; Tengbo YU ; Jinhai TAN ; Xi CHEN ; Fengfei LIN ; Zhangyuan LIN ; Dongfa LIAO ; Aiguo WANG ; Shiwu DONG ; Gaoxing LUO ; Zhao XIE ; Dong SUN ; Dehao FU ; Yunfeng CHEN ; Changqing ZHANG ; Kun LIU ; Deye SONG ; Yongjun RUI ; Fei WU ; Ximing LIU ; Junwen WANG ; Meng ZHAO ; Biao CHE ; Bing HU ; Chengjian HE ; Guanglin WANG ; Xiao CHEN ; Guandong DAI ; Shiyuan FANG ; Wenchao SONG ; Ming CHEN ; Guanghua GUO ; Yongqing XU ; Lei YANG ; Wenqian ZHANG ; Kun ZHANG ; Xin TANG ; Hua CHEN ; Weiguo XU ; Shuquan GUO ; Yong LIU ; Xiaodong GUO ; Zhewei YE ; Liming XIONG ; Tian XIA ; Hongbin WU ; Qisheng ZHOU ; Mengfei LIU ; Yiqiang HU ; Yanjiu HAN ; Hang XUE ; Kangkang ZHA ; Wei CHEN ; Zhiyong HOU ; Bin YU ; Jiacan SU ; Peifu TANG ; Baoguo JIANG ; Guohui LIU
Chinese Journal of Trauma 2025;41(5):421-432
Postoperative infection of internal fixation of closed fractures the lower limbs in adults represents a devastating complication, characterized by diagnostic challenges, prolonged treatment duration and high disability rates. Current management of these infections faces multiple challenges, such as difficulties in early accurate diagnosis, and various controversies about the treatment plan, leading to poor overall diagnosis and treatment results. To address these issues, based on evidence-based medicine and principles with emphasis on scientific rigor, clinical applicability and innovation, the Trauma Branch of the Chinese Medical Association, Orthopedic Branch of the Chinese Medical Doctor Association, Orthopedics Branch of the Chinese Medical Association, and Trauma Orthopedics and Polytrauma Group of the Resuscitation and Emergency Committee of the Chinese Medical Doctor Association have collaboratively organized a panel of relevant experts to develop the Guideline for diagnosis and treatment of infection after internal fixation of closed lower limb fractures in adults ( version 2025). The guideline proposed 10 recommendations, aiming to provide a foundation for standardized diagnosis and treatment of postoperative infection in adults with closed lower limb fractures.
4.Expert Consensus on the Ethical Requirements for Generative AI-Assisted Academic Writing
You-Quan BU ; Yong-Fu CAO ; Zeng-Yi CHANG ; Hong-Yu CHEN ; Xiao-Wei CHEN ; Yuan-Yuan CHEN ; Zhu-Cheng CHEN ; Rui DENG ; Jie DING ; Zhong-Kai FAN ; Guo-Quan GAO ; Xu GAO ; Lan HU ; Xiao-Qing HU ; Hong-Ti JIA ; Ying KONG ; En-Min LI ; Ling LI ; Yu-Hua LI ; Jun-Rong LIU ; Zhi-Qiang LIU ; Ya-Ping LUO ; Xue-Mei LV ; Yan-Xi PEI ; Xiao-Zhong PENG ; Qi-Qun TANG ; You WAN ; Yong WANG ; Ming-Xu WANG ; Xian WANG ; Guang-Kuan XIE ; Jun XIE ; Xiao-Hua YAN ; Mei YIN ; Zhong-Shan YU ; Chun-Yan ZHOU ; Rui-Fang ZHU
Chinese Journal of Biochemistry and Molecular Biology 2025;41(6):826-832
With the rapid development of generative artificial intelligence(GAI)technologies,their widespread application in academic research and writing is continuously expanding the boundaries of sci-entific inquiry.However,this trend has also raised a series of ethical and regulatory challenges,inclu-ding issues related to authorship,content authenticity,citation accuracy,and accountability.In light of the growing involvement of AI in generating academic content,establishing an open,controllable,and trustworthy ethical governance framework has become a key task for safeguarding research integrity and maintaining trust within the academic community.This expert consensus outlines ethical requirements across key stages of AI-assisted academic writing-including topic selection,data management,citation practices,and authorship attribution.It aims to clarify the boundaries and ethical obligations surrounding AI use in academic writing,ensuring that technological tools enhance efficiency without compromising in-tegrity.The goal is to provide guidance and institutional support for building a responsible and sustainable research ecosystem.
5.Comparison of the toxicity and safety of protein derivatives from novel fusion strains of Mycobacterium tuberculosis
Hao-qi XU ; Jiang-tao DONG ; Jie ZHANG ; Fang WU ; Su LIANG ; Xiao-ling LIU ; Lan-ru GAO ; Ju WANG ; Hui ZHANG ; Jiang-dong WU ; Le ZHANG ; Xi-ling DENG ; Wan-jiang ZHANG
Chinese Journal of Zoonoses 2025;41(4):376-384
The objective of this study was to evaluate the toxicity and safety of novel Mycobacterium tuberculosis fusion strain protein derivatives,referred to as B/R strain active proteins.In cellular experiments,RAW264.7 cells were treated with each vaccine preparation,and apoptosis rates were measured.In subsequent animal experiments,C57BL/6 mice were immunized via subcutaneous injection,and their survival and body weight changes were monitored and recorded at 2,4,8,12,and 16 weeks.The lungs and spleens were harvested to calculate organ coefficients,and pathological examinations were conducted.At the eighth week of immunization,the mice were infected with high concentrations of BCG,and pathological changes in the lungs and spleens were observed 4 weeks post-infection.The apoptosis rate at 6 hours was significantly higher in the experimental group than the PBS group(P<0.05).At 12 and 24 hours,the apoptosis rate in the experimental group remained higher than that in the PBS group,although this difference was not statistically significant.After immunization,mice in all four groups exhibited normal growth patterns,as indicated by stable body weight changes.At 4 and 12 weeks post-immunization,the lung coefficients in the protein group were significantly higher than those in the PBS group at the same time points.Additionally,the lung coefficients in the BCG group were significantly elevated across all time periods(P<0.05).The spleen coefficients in the protein and BCG groups were significantly higher than those in the PBS group at 2,4,8,12,and 16 weeks,whereas the ICD B/R group showed higher spleen coefficients than the PBS group only at week 8(P<0.05).Pathological examination revealed normal lung and spleen tissues in the PBS group.However,during the 2-8 weeks immunization period,lung and spleen tissues in all experimental groups exhibited varying degrees of damage,which gradually diminished by 12-16 weeks.Notably,no tuberculosis nodules were observed in any experimental group.After infection with high concentrations of BCG,no overt pathological changes were observed on the surfaces of the lungs and spleens in any group.Microscopic examination revealed less severe pathological changes in the lungs and spleens of mice in the experimental groups than the PBS group.Furthermore,no statistically significant differences were observed between the protein group and the BCG group.Our findings suggested that the B/R strain active proteins'toxicity and safety profiles were comparable to those of BCG,and showed immunoprotective effects.This study provides an experimental foundation for the development of a novel tuberculosis vaccine.
6.Performance validation and result analysis of bioinformatics procedure for metagenomic next-generation sequencing
Wen XI ; Yang XIAO ; Shangdong YANG ; Zhe LIU ; Fang WANG ; Xiaoqin WANG
Chinese Journal of Laboratory Medicine 2025;48(1):117-124
Objective:To establish a preliminary performance validation protocol for the bioinformatics procedure of metagenomic next-generation sequencing (mNGS) in clinical laboratories.Methods:Three types of simulated datasets were designed and the CatⅠ dataset mainly consisted of pathogen reference genomes and human sequences. CatⅠA was a dataset composed of common pathogens mixed with human sequences and was used to evaluate the inclusiveness, accuracy, recall rates, precision, F1-Score, and other indicators of the mNGS bioinformatics procedure. CatⅠB was a dataset composed of closely related species of common pathogens mixed with human sequences, which was used to evaluate the discriminating ability of closely related species of bioinformatics procedure by calculating the detection rates and the relative abundance ratio of closely related species. The real data of 200 clinical samples was selected to construct CatⅡ and the simulated dataset consisted of colonized bacteria, experimental environment bacteria, reagent engineering bacteria, pathogen reference genomes, and human sequences, which was used to evaluate the sensitivity, specificity, and accuracy of bioinformatics pipeline for pathogens detection. The CatⅢ dataset was obtained from the negative bronchoalveolar lavage fluid BALF sequencing data mixed with 20 rare pathogens sequences in order to evaluate the positive detection rates and recall rates of rare pathogens in the bioinformatics analysis.Results:The analysis of the CatⅠA dataset showed that the positive consistency rate, inclusiveness, precision and accuracy of the bioinformatics peocedure under three sequence gradients were all greater than 99%, with a recall rate of 72.31% (95% CI 69.61%-75.01%) and a F1 Score of 82.00% (95% CI 79.77%-84.22%). In the CatⅠB dataset, the closely related species could be effectively detected at all sequence and proportion gradients, and the relative abundance ratio of closely related species was within 2 times of the design ratio except for the coronavirus, haemophilus, primate bocaparvovirus, human respiratory syncytial virus, and eimeria, indicating good ability to identify the closely related species. All the 24 species of pathogens included in CatⅡ dataset were effectively detected, with the sensitivity, specificity, and accuracy all greater than 90%. All rare pathogens were detected in the CatⅢ dataset, with a detection rate of 100%. Conclusions:With the simulated datasets, the performance validation scheme for the mNGS bioinformatics analysis was preliminary established and could evaluate the accuracy of sequence classification, the ability to identify the closely related species, and detection ability of common and rare pathogens, which may provide some references for the construction of mNGS process.
7.Polarized light microscopic mineral phase authentication and health risk assessment of raw and calcined fossil mineral Chinese medicinal material Draconis Os.
Yan-Qiong PAN ; Zheng LIU ; Li-Wen ZHENG ; Ying ZHANG ; Liu ZHOU ; Xi-Long QIAN ; Fang FANG ; Xiao WU ; Sheng-Jin LIU
China Journal of Chinese Materia Medica 2025;50(15):4238-4247
This study aims to investigate the polarized microscopic mineral phase characteristics, inorganic element content, and potential health risks associated with the intake of raw and calcined fossil mineral Chinese medicinal material Draconis Os. Microscopy was employed to observe the mineralogical characteristics of Draconis Os and compare the microscopic features and phase composition of raw and calcined Draconis Os under monochromatic and orthogonal polarized light. Inductively coupled plasma mass spectrometry(ICP-MS) was employed to determine the content of 30 inorganic elements. Health risk assessment was conducted by calculating the single pollution index(P_i), average daily intake of elements for adults(ADI), target hazard quotient(THQ), non-carcinogenic assessment method-hazard quotient(HQ), and the carcinogenic risk of elements(CR). The results indicated that under monochromatic polarized light, the Draconis Os powder sections exhibited light gray-brown to gray-brown irregular fragments, some with undulating textures that were slightly curved. Under crossed polarized light, they appeared dark gray, grayish-white, and yellowish-white. Clear apatite was visible in the ground sections of Draconis Os under crossed polarized light. P_i results indicated that Draconis Os samples were free from contamination and were of good quality. According to the maximum allowable limits of heavy metals stipulated in ISO Traditional Chinese Medicine: Determination of heavy metals in herbal medicines used in Traditional Chinese Medicine, ADI, THQ, HQ, and CR were taken as assessment indicators. Only the THQ value for As(arsenic) in raw Draconis Os was greater than 1, while the THQ values for other heavy metal elements in the Draconis Os samples were all less than 1. The study demonstrates that the primary mineral phase of raw and calcined Draconis Os is apatite, with some samples co-existing with calcite, which can serve as one of the means for quality control of Draconis Os. The elemental analysis results from ICP-MS provide scientific evidence for the safety assessment of Draconis Os, indicating that Draconis Os is safe in clinical application.
Drugs, Chinese Herbal/analysis*
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Risk Assessment
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Minerals/chemistry*
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Fossils
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Humans
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Drug Contamination
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Mass Spectrometry
8.Longitudinal Associations between Vitamin D Status and Systemic Inflammation Markers among Early Adolescents.
Ting TANG ; Xin Hui WANG ; Xue WEN ; Min LI ; Meng Yuan YUAN ; Yong Han LI ; Xiao Qin ZHONG ; Fang Biao TAO ; Pu Yu SU ; Xi Hua YU ; Geng Fu WANG
Biomedical and Environmental Sciences 2025;38(1):94-99
9.Thermal Ablation of Pulmonary Nodules by Electromagnetic Navigation Bronchoscopy Combined With Real-Time CT-Based 3D Fusion Navigation:Report of One Case.
Yuan XU ; Qun LIU ; Chao GUO ; Yi-Bo WANG ; Xiao-Fang WU ; Chen-Xi MA ; Gui-Ge WANG ; Qian-Shu LIU ; Nai-Xin LIANG ; Shan-Qing LI
Acta Academiae Medicinae Sinicae 2025;47(1):137-141
A nodule in the right middle lobe of the lung was treated by a combination of cone-beam CT,three-dimensional registration for fusion imaging,and electromagnetic navigation bronchoscopy-guided thermal ablation.The procedure lasted for 90 min,with no significant bleeding observed under the bronchoscope.The total radiation dose during the operation was 384 mGy.The patient recovered well postoperatively,with only a small amount of blood in the sputum and no pneumothorax or other complications.A follow-up chest CT on the first day post operation showed that the ablation area completely covered the lesion,and the patient was discharged successfully.
Humans
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Bronchoscopy/methods*
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Catheter Ablation/methods*
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Cone-Beam Computed Tomography
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Electromagnetic Phenomena
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Imaging, Three-Dimensional
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Lung Neoplasms/diagnostic imaging*
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Tomography, X-Ray Computed
10.Psychological stress-activated NR3C1/NUPR1 axis promotes ovarian tumor metastasis.
Bin LIU ; Wen-Zhe DENG ; Wen-Hua HU ; Rong-Xi LU ; Qing-Yu ZHANG ; Chen-Feng GAO ; Xiao-Jie HUANG ; Wei-Guo LIAO ; Jin GAO ; Yang LIU ; Hiroshi KURIHARA ; Yi-Fang LI ; Xu-Hui ZHANG ; Yan-Ping WU ; Lei LIANG ; Rong-Rong HE
Acta Pharmaceutica Sinica B 2025;15(6):3149-3162
Ovarian tumor (OT) is the most lethal form of gynecologic malignancy, with minimal improvements in patient outcomes over the past several decades. Metastasis is the leading cause of ovarian cancer-related deaths, yet the underlying mechanisms remain poorly understood. Psychological stress is known to activate the glucocorticoid receptor (NR3C1), a factor associated with poor prognosis in OT patients. However, the precise mechanisms linking NR3C1 signaling and metastasis have yet to be fully elucidated. In this study, we demonstrate that chronic restraint stress accelerates epithelial-mesenchymal transition (EMT) and metastasis in OT through an NR3C1-dependent mechanism involving nuclear protein 1 (NUPR1). Mechanistically, NR3C1 directly regulates the transcription of NUPR1, which in turn increases the expression of snail family transcriptional repressor 2 (SNAI2), a key driver of EMT. Clinically, elevated NR3C1 positively correlates with NUPR1 expression in OT patients, and both are positively associated with poorer prognosis. Overall, our study identified the NR3C1/NUPR1 axis as a critical regulatory pathway in psychological stress-induced OT metastasis, suggesting a potential therapeutic target for intervention in OT metastasis.

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