1.TPMGD: A genomic database for the traditional medicines in Pakistan.
Rushuang XIANG ; Huihua WAN ; Wei SUN ; Baozhong DUAN ; Weiqian CHEN ; Xue CAO ; Sifan WANG ; Chi SONG ; Shilin CHEN ; Yan WANG ; Atia-Tul WAHAB ; M IQBAL CHOUDHARY ; Xiangxiao MENG
Chinese Herbal Medicines 2025;17(1):87-93
OBJECTIVE:
In Pakistan, traditional medicines are an important component of the medical system, with numerous varieties and great demands. However, due to the scattered resources and the lack of systematic collection and collation, adulteration of traditional Pakistani medicine (TPM) is common, which severely affects the safety of their medicinal use and the import and export trades. Therefore, it is urgent to systematically organize and unify the management of TPM and establish a set of standards and operable methods for the identification of TPM.
METHODS:
We collected and organized the information on 128 TPMs with regard to their medicinal parts, efficacy, usage, and genetic material, based on Pakistan Hamdard Pharmacopoeia of Eastern Medicine: Pharmaceutical Codex. The genetic information of TPM is summarized from national center for biotechnology information (NCBI) and global pharmacopoeia genome database (GPGD). Furthermore, we utilized bioinformatics technology to supplement the chloroplast genome (cp-genome) data of 12 TPMs. To build the web server, we used the Linux + Apache + MySQL + PHP (LAMP) system and constructed the webpage on a PHP: Hypertext Preprocessor (PHP) model view controller (MVC) framework.
RESULTS:
We constructed a new genomic database, the traditional Pakistani medicine genomic database (TPMGD). This database comprises five entries, namely homepage, medicinal species, species identification, basic local alignment search tool (BLAST), and download. Currently, TPMGD contains basic profiles of 128 TPMs and genetic information of 102 TPMs, including 140 cytochrome c oxidase subunit I (COI) sequences and 119 mitochondrial genome sequences from Bombyx mori, 1 396 internal transcribed spacer 2 (ITS2) sequences and 1 074 intergenic region (psbA-trnH) sequences specific to 92 and 83 plant species, respectively. Additionally, TPMGD includes 199 cp-genome sequences of 82 TPMs.
CONCLUSION
TPMGD is a multifunctional database that integrates species description, functional information inquiry, genetic information storage, molecular identification of TPM, etc. The database not only provides convenience for TPM information queries but also establishes the scientific basis for the medication safety, species identification, and resource protection of TPM.
2.Research Advances in the Construction and Application of Intestinal Organoids.
Qing Xue MENG ; Hong Yang YI ; Peng WANG ; Shan LIU ; Wei Quan LIANG ; Cui Shan CHI ; Chen Yu MAO ; Wei Zheng LIANG ; Jun XUE ; Hong Zhou LU
Biomedical and Environmental Sciences 2025;38(2):230-247
The structure of intestinal tissue is complex. In vitro simulation of intestinal structure and function is important for studying intestinal development and diseases. Recently, organoids have been successfully constructed and they have come to play an important role in biomedical research. Organoids are miniaturized three-dimensional (3D) organs, derived from stem cells, which mimic the structure, cell types, and physiological functions of an organ, making them robust models for biomedical research. Intestinal organoids are 3D micro-organs derived from intestinal stem cells or pluripotent stem cells that can successfully simulate the complex structure and function of the intestine, thereby providing a valuable platform for intestinal development and disease research. In this article, we review the latest progress in the construction and application of intestinal organoids.
Organoids/cytology*
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Intestines/physiology*
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Humans
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Animals
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Pluripotent Stem Cells
3.pLM4ACP: a model for predicting anticancer peptides based on machine learning and protein language models.
Yitong LIU ; Wenxin CHEN ; Juanjuan LI ; Xue CHI ; Xiang MA ; Yanqiong TANG ; Hong LI
Chinese Journal of Biotechnology 2025;41(8):3252-3261
Cancer is a serious global health problem and a major cause of human death. Conventional cancer treatments often run the risk of impairing vital organ functions. Anticancer peptides (ACPs) are considered to be one of the most promising therapeutic agents against common human cancers due to their small sizes, high specificity, and low toxicity. Since ACP recognition is highly limited to the laboratory, expensive, and time-consuming, we proposed pLM4ACP, a model for predicting ACPs based on machine learning and protein language models. In this model, the protein language model ProtT5 was used to extract the features of ACPs, and the extracted features were input into the support vector machine (SVM) classification algorithm for optimization and performance evaluation. The model showcased significantly higher accuracy than other methods, with the overall accuracy of 0.763, F1-score of 0.767, Matthews correlation coefficient of 0.527, and area under the curve of 0.827 on the independent test set. This study constructs an efficient anticancer peptide prediction model based on protein language models, further advancing the application of artificial intelligence in the biomedical field and promoting the development of precision medicine and computational biology.
Machine Learning
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Antineoplastic Agents/chemistry*
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Humans
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Peptides/chemistry*
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Support Vector Machine
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Algorithms
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Computational Biology/methods*
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Neoplasms/drug therapy*
4.Application and challenge of immunotherapy in perioperative therapy of gastric cancer
Chi XUE ; Peng GAO ; Zhi ZHU ; Zhenning WANG
China Oncology 2024;34(3):259-267
Gastric cancer is one of the common malignant tumors of digestive system in our country.The proportion of patients in advanced and late stage is large,and the choice of perioperative treatment program is always difficult in clinic.For most locally advanced gastric cancer,compared with standard radical surgery combined with postoperative adjuvant chemotherapy,perioperative treatment mode may further improve the survival of patients.However,the efficacy of conventional chemotherapy regimen has reached a plateau,while the progress of traditional molecular targeted therapy is relatively slow.In recent years,with the increasing role of immunotherapy in the treatment of advanced gastric cancer,more and more clinical studies have shown that immunotherapy can also achieve better efficacy in perioperative gastric cancer patients.This article reviewed the research progress of immunotherapy in perioperative gastric cancer in recent years.
5.Phosphatidylinositol 3-kinases Play a Suppressive Role in Electrotaxis of Dictyostelium Cells Through Akt and ERK
Xiao-Xue GE ; Rui-Da JIANG ; Xiao-Yan WANG ; Jing GAO ; Run-Chi GAO
Progress in Biochemistry and Biophysics 2024;51(3):685-695
ObjectivePhosphatidylinositol 3 kinases (PI3Ks) play an important role in cell directional movement by regulating F-actin. However, the structure and function of PI3Ks are complex. The role of PI3Ks in cell electrotaxis is not fully understood. Therefore, in this study, the model organism Dictyostelium discoideum cells were used as experimental materials to explore the role of PI3K1 and PI3K2 in electrotaxis. MethodsFirstly, PI3K1 coding gene pikA knockout mutant and PI3K2 coding gene pikB knockout mutant were constructed by CRISPR/Cas9 system. Secondly, two mutants were placed in a DC electric field with a strength of 12 V/cm and the electrotaxis were analyzed. ResultsData analysis showed that the direction index of wild-type cells in DC electric field was (0.86±0.03), while the direction index of pikA- and pikB- mutants in DC electric field was (0.95±0.02) and (0.94±0.03), respectively. In addition, the average trajectory speed of wild-type cells in the electric field was (3.34±0.08) μm/min, while the average trajectory speed of pikA- and pikB- mutants were (4.85±0.20) μm/min and (5.48±0.15) μm/min, respectively. The t test showed that there were significant differences in the directedness index and speed between the mutant and wild type. Western blot results showed that both phosphorylated Akt and phosphorylated ERK were significantly increased in pikA- and pikB- mutants. ConclusionPI3K1 and PI3K2 may inhibit the electrotaxis of Dictyostelium discoideum cells by increasing the activity of Akt and ERK.
6.Mechanism of Chinese medicine for promoting blood circulation and removing blood stasis combined with platelet-rich plasma to improve steroid-induced necrosis of the femoral head
Chengming LI ; Dongling XUE ; Xinyu YANG ; Chi XIAO ; Daping CUI
Chinese Journal of Tissue Engineering Research 2024;28(2):288-294
BACKGROUND:At present,it is found that both Chinese medicine for activating blood circulation and removing blood stasis and platelet-rich plasma technology can repair damaged blood vessels,promote vascular regeneration,rebuild blood supply in the femoral head,restore normal blood supply,and further promote osteogenesis.Both of them have certain advantages in early intervention of steroid-induced necrosis of femoral head.It can also further understand the mechanism of blood activating and stasis removing herbs and platelet-rich plasma technology in improving steroid-induced necrosis of the femoral head,and provide new ideas for future treatment. OBJECTIVE:To review the research progress of the mechanism of the combination of blood activating and blood stasis removing herbs and platelet-rich plasma technology on steroid-induced necrosis of the femoral head according to the related literature at home and abroad. METHODS:PubMed,Web of Science,Metstr,CNKI and WanFang databases were searched for relevant articles."Traditional Chinese medicine,signal pathways,steroid induced necrosis of femoral head,vascular endothelial growth factor,platelet rich plasma"were used as the Chinese and English search terms separately.The time limit for searching the literature was from January 2000 to July 2022,and 75 related articles were finally included. RESULTS AND CONCLUSION:Both Chinese medicine for activating blood circulation and removing blood stasis and platelet-rich plasma technology have certain advantages in intervening the early stage of steroid-induced necrosis of femoral head.For traditional Chinese medicine,both single and compound drugs can effectively alleviate the further development of steroid-induced necrosis of the femoral head.The specific mechanism is as follows:(1)The traditional Chinese medicine for activating blood circulation and removing blood stasis has a significant anticoagulation effect,which can antagonize the abnormal(hypercoagulable)state of blood caused by hormone drugs,and further restore the normal blood supply in the femoral head.(2)Traditional Chinese medicine for activating blood circulation and removing blood stasis can repair damaged vascular endothelium,regenerate blood vessels and remodel blood supply in the femoral head by activating vascular endothelial growth factor.(3)The traditional Chinese medicine of promoting blood circulation and removing blood stasis has the obvious effect of removing blood stasis,which can reduce the accumulation of fat cells in the bone marrow cavity and relieve the pressure in the femoral head.(4)Traditional Chinese medicine for promoting blood circulation and removing blood stasis can regulate relevant signal pathways,maintain bone metabolism,promote the differentiation and balance of osteoblasts and osteoclasts,and effectively reduce steroid-induced necrosis of the femoral head.In addition,platelet-rich plasma contains a large amount of high concentration of cell growth factor,which plays a positive role in osteogenesis and vascular regeneration,and can also improve the abnormal state of the blood.Traditional Chinese medicine for activating blood circulation and removing blood stasis combined with platelet-rich plasma technology can play their biological roles,and the intervention effect is more significant.
7.Bladder large cell lymphoma: a case report and literature review
Hao WANG ; Butang LI ; Chenfei CHI ; Xincheng JIANG ; Weijing YE ; Qi CHEN ; Guoliang YANG ; Wei XUE
Journal of Modern Urology 2024;29(2):122-125
【Objective】 To improve the understanding and diagnosis and treatment level of ALK negative anaplastic large cell lymphoma (ALK-ALCL) by sharing the diagnosis and treatment process of a patient with ALK-ALCL treated in Hangzhou Bay Hospital of Ningbo. 【Methods】 The clinical data and diagnosis and treatment process of the patient were retrospectively analyzed, and relevant literature was reviewed. 【Results】 The patient was a young male, with recurrent gross hematuria and right low back pain as the initial symptoms.Imaging examination indicated bladder tumor.After resection, the tumor was reduced and confirmed to be ALK-ALCL.After chemotherapy and autologous hematopoietic stem cell transplantation, the patient’s condition continued to improve.During the follow-up, no recurrence was observed. 【Conclusion】 Primary ALK-ALCL in the bladder is very rare and prone to misdiagnosis and missed diagnosis in clinical practice.The successful diagnosis and treatment experience of this patient can provide clinical reference.
8.Identification of genes related to prognosis of retroperi-toneal liposarcoma based on transcriptome sequencing
Chang-Chun YE ; Miao-Miao CHI ; Yan-Sheng HU ; Ge LI ; Xue-Jun SUN ; Qi SUN
Chinese Journal of Current Advances in General Surgery 2024;27(4):292-297
Objective:To analyze and compare the differences of expression profiles between RPL and normal adipose tissue by transcriptome sequencing(RNA-Seq),then identify the key genes related to prognosis and explore their potential mechanisms.Methods:Tumor tissues and normal adipose tissues of patients with RPL were collected for RNA-Seq,and then the differentially ex-pressed genes were analyzed by GO and KEGG enrichment analysis.Based on TCGA,the high-risk genes related to prognosis were screened and verified by Kaplan-Meier curve and receiver operat-ing characteristic(ROC)curve.Results:Compared with normal adipose tissue,279 differentially expressed genes were simultaneously up-regulated in RPL tissues,which were mainly enriched in immune response and PPAR signaling pathway.Combined with TCGA,7 stable prognostic high risk genes were identified and the overall survival rate of the high risk group was significantly lower than that of the low risk group(P<0.05).Conclusion:KCNQ5,RBPJ and some other genes may be re-lated to the poor prognosis of RPL patients.The analysis of the mechanism of these genes in RPL is expected to provide new evidence for the formulation of diagnosis and treatment strategies for RPL patients.
9.Research Progress on Dental Age Estimation Based on MRI Technology
Lei SHI ; Ye XUE ; Li-Rong QIU ; Ting LU ; Fei FAN ; Yu-Chi ZHOU ; Zhen-Hua DENG
Journal of Forensic Medicine 2024;40(2):112-117
Dental age estimation is a crucial aspect and one of the ways to accomplish forensic age estimation,and imaging technology is an important technique for dental age estimation.In recent years,some studies have preliminarily confirmed the feasibility of magnetic resonance imaging(MRI)in evaluating dental development,providing a new perspective and possibility for the evaluation of den-tal development,suggesting that MRI is expected to be a safer and more accurate tool for dental age estimation.However,further research is essential to verify its accuracy and feasibility.This article re-views the current state,challenges and limitations of MRI in dental development and age estimation,offering reference for the research of dental age assessment based on MRI technology.
10.Investigating age-related characteristics of gait parameters in community-dwelling older adults during normal walking
Ji SHEN ; Yuting KANG ; Hongyu LI ; Jing PANG ; Jie ZHANG ; Chi ZHANG ; Xue MENG ; Guoqing FAN ; Hong SHI
Chinese Journal of Geriatrics 2024;43(11):1468-1474
Objective:To investigate age-related characteristics of gait parameters in the elderly.Methods:From February 2023 to August 2023, a convenient sampling method was used to investigate the elderly over 60 years old in communities in Beijing.General characteristics and anthropometric data were collected.Gait parameters of the subjects during normal speed walking were measured using a wearable gait analyzer.Comparisons were made of the basic characteristics, physical status and gait parameters in different age groups.Linear regression analysis was used to evaluate the changes of physical status and gait parameters with age, with the 60-69-year-old group as the baseline standard.Results:A total of 670 elderly people were included, including 324(48.4%)aged 60-69 years, 285(42.5%)aged 70-79 years, and 61(9.1%)aged ≥80 years.Linear regression analysis showed that after adjusting for confounding factors, with increasing age, skeletal muscle mass index(SMI)( β=-0.018, 95% CI: -0.029--0.007), calf circumference( β=-0.096, 95% CI: -0.142--0.051), upper limb flexibility( β=-0.200, 95%, 95% CI: -0.355--0.046), lower limb flexibility( β=-0.244, 95% CI: -0.377--0.111), grip strength( β=-0.397, 95% CI: -0.491--0.303), the Short Physical Performance Battery(SPPB)( β=-0.080, 95% CI: -0.100--0.060)decreased( P<0.05), and the gait parameter such as speed( β=-0.010, 95% CI: -0.014--0.007), cadence( β=-0.398, 95% CI: -0.634--0.162), step length/height( β=-0.002, 95% CI: -0.003--0.002), stride length( β=-0.009, 95% CI: -0.011--0.007), swing power( β=-0.009, 95% CI: -0.012--0.006), ground impact( β=-0.020, 95% CI: -0.026--0.014), foot fall( β=-0.050, 95% CI: -0.064--0.036), pre-swing angle( β=-0.545, 95% CI: -0.714--0.377)all decreased( P<0.05), while stride time( β=0.005, 95% CI: 0.001-0.009), single limb support time( β=1.566, 95% CI: 0.499-2.633), terminal double limb support time( β=0.609, 95% CI: 0.084-1.134), swing duration( β=1.288, 95% CI: 0.024-2.552), single step time( β=2.417, 95% CI: 0.462-4.372)and support phase time( β=1.935, 95% CI: 0.421-3.449)all increased( P<0.05). Conclusions:The walking ability tends to decline with age in older people in the community who walk at a normal walking speed.

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