1.Alternative Polyadenylation in Mammalian
Yu ZHANG ; Hong-Xia CHI ; Wu-Ri-Tu YANG ; Yong-Chun ZUO ; Yong-Qiang XING
Progress in Biochemistry and Biophysics 2025;52(1):32-49
With the rapid development of sequencing technologies, the detection of alternative polyadenylation (APA) in mammals has become more precise. APA precisely regulates gene expression by altering the length and position of the poly(A) tail, and is involved in various biological processes such as disease occurrence and embryonic development. The research on APA in mammals mainly focuses on the following aspects:(1) identifying APA based on transcriptome data and elucidating their characteristics; (2) investigating the relationship between APA and gene expression regulation to reveal its important role in life regulation;(3) exploring the intrinsic connections between APA and disease occurrence, embryonic development, differentiation, and other life processes to provide new perspectives and methods for disease diagnosis and treatment, as well as uncovering embryonic development regulatory mechanisms. In this review, the classification, mechanisms and functions of APA were elaborated in detail and the methods for APA identifying and APA data resources based on various transcriptome data were systematically summarized. Moreover, we epitomized and provided an outlook on research on APA, emphasizing the role of sequencing technologies in driving studies on APA in mammals. In the future, with the further development of sequencing technology, the regulatory mechanisms of APA in mammals will become clearer.
2.Artificial intelligence in prostate cancer.
Wei LI ; Ruoyu HU ; Quan ZHANG ; Zhangsheng YU ; Longxin DENG ; Xinhao ZHU ; Yujia XIA ; Zijian SONG ; Alessia CIMADAMORE ; Fei CHEN ; Antonio LOPEZ-BELTRAN ; Rodolfo MONTIRONI ; Liang CHENG ; Rui CHEN
Chinese Medical Journal 2025;138(15):1769-1782
Prostate cancer (PCa) ranks as the second most prevalent malignancy among men worldwide. Early diagnosis, personalized treatment, and prognosis prediction of PCa play a crucial role in improving patients' survival rates. The advancement of artificial intelligence (AI), particularly the utilization of deep learning (DL) algorithms, has brought about substantial progress in assisting the diagnosis, treatment, and prognosis prediction of PCa. The introduction of the foundation model has revolutionized the application of AI in medical treatment and facilitated its integration into clinical practice. This review emphasizes the clinical application of AI in PCa by discussing recent advancements from both pathological and imaging perspectives. Furthermore, it explores the current challenges faced by AI in clinical applications while also considering future developments, aiming to provide a valuable point of reference for the integration of AI and clinical applications.
Humans
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Prostatic Neoplasms/diagnosis*
;
Male
;
Artificial Intelligence
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Deep Learning
;
Prognosis
3.Identification and expression analysis of AP2/ERF family members in Lonicera macranthoides.
Si-Min ZHOU ; Mei-Ling QU ; Juan ZENG ; Jia-Wei HE ; Jing-Yu ZHANG ; Zhi-Hui WANG ; Qiao-Zhen TONG ; Ri-Bao ZHOU ; Xiang-Dan LIU
China Journal of Chinese Materia Medica 2025;50(15):4248-4262
The AP2/ERF transcription factor family is a class of transcription factors widely present in plants, playing a crucial role in regulating flowering, flower development, flower opening, and flower senescence. Based on transcriptome data from flower, leaf, and stem samples of two Lonicera macranthoides varieties, 117 L. macranthoides AP2/ERF family members were identified, including 14 AP2 subfamily members, 61 ERF subfamily members, 40 DREB subfamily members, and 2 RAV subfamily members. Bioinformatics and differential gene expression analyses were performed using NCBI, ExPASy, SOMPA, and other platforms, and the expression patterns of L. macranthoides AP2/ERF transcription factors were validated via qRT-PCR. The results indicated that the 117 LmAP2/ERF members exhibited both similarities and variations in protein physicochemical properties, AP2 domains, family evolution, and protein functions. Differential gene expression analysis revealed that AP2/ERF transcription factors were primarily differentially expressed in the flowers of the two L. macranthoides varieties, with the differentially expressed genes mainly belonging to the ERF and DREB subfamilies. Further analysis identified three AP2 subfamily genes and two ERF subfamily genes as potential regulators of flower development, two ERF subfamily genes involved in flower opening, and two ERF subfamily genes along with one DREB subfamily gene involved in flower senescence. Based on family evolution and expression analyses, it is speculated that AP2/ERF transcription factors can regulate flower development, opening, and senescence in L. macranthoides, with ERF subfamily genes potentially serving as key regulators of flowering duration. These findings provide a theoretical foundation for further research into the specific functions of the AP2/ERF transcription factor family in L. macranthoides and offer important theoretical insights into the molecular mechanisms underlying floral phenotypic differences among its varieties.
Plant Proteins/chemistry*
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Gene Expression Regulation, Plant
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Transcription Factors/chemistry*
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Lonicera/classification*
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Flowers/metabolism*
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Phylogeny
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Gene Expression Profiling
;
Multigene Family
4.Efficacy Analysis of Stanozolol Combined with Avatrombopag in the Treatment of Chemotherapy-Induced Thrombocytopenia in Relapsed/Refractory Tumors.
Yan HE ; Wei-Yi LIU ; Yan-Yu ZHANG ; Yan LYU ; Shan-Shan ZHANG ; Ri-Cheng QUAN
Journal of Experimental Hematology 2025;33(4):1127-1130
OBJECTIVE:
To investigate the efficacy and safety of stanozolol combined with avatrombopag in the treatment of chemotherapy-induced thrombocytopenia (CIT) in patients with relapsed/refractory tumors.
METHODS:
Twenty-five patients with relapsed/refractory CIT admitted to the Hematology Department of Xiyuan Hospital, China Academy of Chinese Medical Sciences between March 2023 to December 2023 were enrolled. These patients received a combined therapy of stanozolol and avatrombopag. The clinical efficacy, onset time, changes in platelet levels and blood cell counts before and after treatment, and adverse reactions of patients were evaluated.
RESULTS:
The combination therapy demonstrated remarkable efficacy with a total effective rate of 100%. Among the 25 patients, 19 achieved complete remission and 6 achieved partial remission. The median onset time was 42.5(range: 35-48)days. The average platelet count of the 25 patients increased from (25.73±17.75)×109/L before treatment to (146.4±49.59)×109/L after 3 months of treatment, with a statistically significant difference ( P < 0.05). 18 patients who previously required platelet transfusion were all weaned off platelet transfusion after 3 months of treatment, with a median time to be free from platelet transfusion was 26 (range: 18-51) days. During the treatment, both neutrophils and hemoglobin exhibited various degrees of elevation. Two patients experienced a slight increase in alanine aminotransferase(ALT) levels, which normalized after treatment with oral hepatoprotective drug. One patient had a PLT increase exceeding 350×109/L, and the treatment with avatrombopag was suspended, and aspirin and other drugs were given to prevent thrombosis. No thrombose events or CIT-related bleeding events were observed in all patients.
CONCLUSION
The combination therapy of stanozolol and avatrombopag is significantly effective for treating relapsed/refractory CIT patients, with a high response rate and good safety, making it a suitable clinical treatment option.
Humans
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Thrombocytopenia/chemically induced*
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Stanozolol/therapeutic use*
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Male
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Female
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Neoplasms/drug therapy*
;
Middle Aged
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Thiophenes/therapeutic use*
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Adult
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Platelet Count
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Treatment Outcome
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Antineoplastic Agents/adverse effects*
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Recurrence
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Thiazoles
5.Artificial Intelligence in Diagnostics: Enhancing Urine Test Accuracy Using a Mobile Phone–Based Reading System
Hyun Jin KIM ; Manmyung KIM ; Hyunjae ZHANG ; Hae Ri KIM ; Jae Wan JEON ; Yuri SEO ; Qute CHOI
Annals of Laboratory Medicine 2025;45(2):178-184
Background:
Urinalysis, an essential diagnostic tool, faces challenges in terms of standardization and accuracy. The use of artificial intelligence (AI) with mobile technology can potentially solve these challenges. Therefore, we investigated the effectiveness and accuracy of an AI-based program in automatically interpreting urine test strips using mobile phone cameras, an approach that may revolutionize point-of-care testing.
Methods:
We developed novel urine test strips and an AI algorithm for image capture.Sample images from the Chungnam National University Sejong Hospital were collected to train a k-nearest neighbor classification algorithm to read the strips. A mobile application was developed for image capturing and processing. We assessed the accuracy, sensitivity, specificity, and ROC area under the curve for 10 parameters.
Results:
In total, 2,612 urine test strip images were collected. The AI algorithm demonstrated 98.7% accuracy in detecting urinary nitrite and 97.3% accuracy in detecting urinary glucose. The sensitivity and specificity were high for most parameters. However, this system could not reliably determine the specific gravity. The optimal time for capturing the test strip results was 75 secs after dipping.
Conclusions
The AI-based program accurately interpreted urine test strips using smartphone cameras, offering an accessible and efficient method for urinalysis. This system can be used for immediate analysis and remote testing. Further research is warranted to refine test parameters such as specific gravity to enhance accuracy and reliability.
6.Analysis of component composition and content determination of six constituents for Xeriga-4 Powder
Jun LI ; Yue-Wu WANG ; Qian ZHANG ; Ping CUI ; Ri-Gui YE ; Ji-ri-mu-ba-tu
Chinese Traditional Patent Medicine 2024;46(1):14-22
AIM To analyze the component composition of Xeriga-4 Powder,and to determine the contents of phellodendrine,chlorogenic acid,gardenoside,berberine,rutin and curcumin.METHODS The high performance liquid chromatography-Q-exactive orbitrap mass spectrometry(HPLC-Q-Exactive-MS)qualitative analysis was performed on a 35℃thermostatic Agilent ZORBAX SB-Aq column(4.6 mm×150 mm,5 μm),with the mobile phase comprising of methanol-0.1%formic acid flowing at 0.35 mL/min in a gradient elution manner,and electron spray ionization source was adopted in positive and negative ion scanning.High performance liquid chromatography tandem mass spectrometry(HPLC-MS/MS)quantitative analysis was performed on a 35℃thermostatic Shim-pack GIST-HP C18 column(2.1 mm×100 mm,3 μm),with the mobile phase comprising of methanol-0.1%formic acid flowing at 0.25 mL/min in a gradient elution manner,and electron spray ionization source was adopted in positive and negative ion scanning with multiple reaction monitoring mode.RESULTS Total 65 constituents were identified,containing 19 alkaloids,13 organic acids,13 flavonoids,7 curcumins,6 iridoids,4 fatty acids,2 aldehydes,and 1 amino acid.Six constituents showed good linear relationships within their own ranges(r≥0.999 1),whose average recoveries were 96.44%-102.37%with the RSDs of 2.05%-3.74%.CONCLUSION This study can provide a reference for the quality control for Xieriga-4 Powder.
7.A brief analysis of the progress of small field dosimetry technologies in radiotherapy
Renjing LINGHU ; Jing ZHANG ; Runcheng LIANG ; Faguo CHEN ; Ri ZHAO ; Xin LIU
Chinese Journal of Radiological Health 2024;33(4):483-490
Compared with conventional radiotherapy fields, small field has unique dosimetry characteristics such as high dose gradient, charged particle imbalance, and dose effect caused by source occlusion. These characteristics increase the difficulty of dose measurement and thus the uncertainty of clinical dose measurement, far exceeding the requirement of < 5% measurement error in ICRU 24 report. In recent years, with the development of new radiotherapy technologies, the minimum radiotherapy field can reach the millimeter level, and the single irradiation dose of hypofractionated radiotherapy can exceed 6 Gy. The larger dose gradient at the edge of radiotherapy field requires higher accuracy of dose measurement, and accurate small field dosimetry technologies have gradually become a research hotspot in the field of precision radiotherapy. In order to ensure the high accuracy of measurement, this paper reviews the research on small field dosimetry worldwide, and summarizes the key points of small field dosimetry. In this paper, the characteristics of small field dosimetry are introduced, and the current small field dosimetry technologies and optimization methods are summarized, including the optimization of detector selection and detector sensitive volume. The field output correction factor technologies are analyzed. In view of the difficulty in small field dosimetry, this paper provides suggestions on dosimetry based on clinical needs and the characteristics of medical linear accelerators. Our suggestions provide a scientific reference for small field dosimetry in clinical practice in radiotherapy institutions, and facilitate the development of radiotherapy dose verification.
8.Reform and Development of Rare Diseases Drug Evaluation and Approval in China
Guo HUANG ; Zhimin YANG ; Ling TANG ; Jie ZHANG ; Xing AI ; Geleng SE RI ; Tian ZHAO
JOURNAL OF RARE DISEASES 2024;3(4):438-445
Rare diseases have a significant and profound impact on society, the economy, and the healthcare system. The path to developing drugs for rare diseases is particularly arduous. Due to the small number of patients and limited market demand, pharmaceutical companies don′t have enough incentives and resources to invest in drug research and development. Additionally, the long development cycles, high costs, and high risks have led to a number of potential therapeutic drug failures at the early stages of development. This article summarizes a series of encouraging policies adopted by the National Medical Products Administration for rare diseases, which is an important public health issue, as well as the achievements in the review and approval of rare disease drugs in recent years. These policies have accelerated the approval process. Meanwhile, the policies ensure the safety and effectiveness of drugs and offer more treatment options and hopes to patients with rare diseases. With the continuous effort at optimizing the policy environment and the advancement of research and development technologies, China′s drug regulatory authorities will continue to focus on the clinical needs of rare diseases, to implement " patient-centered " approach to drug development, inject new vitality into the research and development of drugs of rare diseases, and offer more precise and effective treatment choices for patients with rare diseases.
9.Chemical constituents from Ligularia duciformis and their anti-inflammatory activities
Ri-Cuo LUO ; Xin-Yu ZHANG ; Guo-Yue ZHONG ; Hong-Ling WANG
Chinese Traditional Patent Medicine 2024;46(6):1882-1888
AIM To study the chemical constituents from Ligularia duciformis(C.Winkl.)Hand.-Mazz.and their anti-inflammatory activities.METHODS The ethanol extract from L.duciformis was isolated and purified by HPLC,gel column and silica gel chromatography,then the structures of obtained compounds were identified by physicochemical properties and spectral data.The anti-inflammatory activities of the compounds in vitro was determined by CCK-8 and Griess methods.RESULTS Eighteen compounds were isolated and identified as 14-acetoxy-7β-senecioyloxy-1-(2-methylbutyryloxy)-notonipetranone(1),rel-(1R,3αS,5R,6S,7R,7αS)-1-[(1S)-1-(acetyloxy)ethyl]octahydro-6-[(2-methylbutanoyl)oxy]-4-methylidene-2-oxo-7-(propan-2-yl)-1H-inden-5-yl(2E)-3-methylpent-2-enoate(2),tussilagone(3),petasipaline B(4),8α-hydroxy-4(15),11-eudesmadiene(5),lupenone(6),lupeol(7),(3[3)-lup-20(29)-en-3-yl stearate(8),pinoresinol monoglucoside(9),isoeucommin A(10),isoline(11),uridine(12),tetratriacontanol(13),palmitic acid(14),tridec-1-ene(15),cis-octadec-9-enoic acid(16),methyl-α-D-fructofuranoside(17),β-sitosterol(18).Compounds 1-6,9-11 and 14 showed inhibitory activities against LPS-induced NO production in RAW264.7 cells.CONCLUSION Compounds 3-6,8-10,12-17 are first isolated from this plant.Compounds 1-6,9-11 and 14 have anti-inflammatory activities.
10.Mechanism Study of Chonghe Soft Extract on Promoting Ulcer Wound Healing in Diabetes Rats Based on Akt-mTOR Autophagy-mediated NLRP3 Inflammasome Inactivation
Ying DANG ; Jianping SHI ; Suo ZHANG ; Yu LIU ; Ri HAI ; Hao WU ; Yuqi JIAO ; Lu WANG ; Jie BAI ; Xu CHEN
Traditional Chinese Drug Research & Clinical Pharmacology 2024;35(6):841-849
Objective To investigate the mechanism of Chonghe soft extract on ulcer wound healing in diabetic rats through protein kinase B(Akt)/mammalian Sirolimus target protein(mTOR)-mediated nucleotides binding oligomeric acid domain-like receptor protein 3(NLRP3)inflammasome inactivation.Methods Thirty six SD rats with diabetic ulcer,which were established by feeding with high glucose and high fat diet and injecting intraperitoneally with streptozocin(STZ)combined with skin defect,were randomly divided into model group,Chonghe soft extract group and growth factor group,with twelve rats in each group.Another twelve SD rats were injected an equal dose of citric acid-sodium citrate buffer solution and used as blank group.The blank group and the model group were not received drug intervention,but the Chonghe soft extract group and the growth factor group were externally applied Chonghe soft extract and growth factor gel,respectively.The wound healing of each group was observed and recorded.After 7 days and 14 days of treatment,the histopathology of wound were observed by HE staining and the number of fibroblasts were counted.The levels of IL-1β,IL-18 and TNF-α in serum were detected by ELISA.The expression of autophagy-related protein Beclin-1 and LC3Ⅱ in granulation tissue was detected by immunohistochemistry.The expression of NLRP3,apoptosis-associated speck-like protein containing a caspase recruitment domain(ASC),Caspase1,Pro-Caspase1 and Akt/mTOR autophagy pathway-related proteins Akt,p-Akt,mTOR and p-mTOR were detected by Western Blot.Results Compared with the blank control group,the pathological wound repair of the model group was delayed on the 7th day and 14th day,the number of fibroblasts per unit area was decreased(P<0.01).The levels of IL-1β,IL-18 and TNF-α were increased(P<0.01).The expression levels of ASC,Pro-Caspase1,Caspase1,and NLRP3 were increased in the wound tissues(P<0.01),while the expression levels of Beclin-1,LC3-Ⅱ,mTOR,p-mTOR,Akt and p-Akt were decreased in the wound tissues(P<0.01).Compared with the model group,the pathological injury in Chonghe soft extract group and growth factor group was significantly improved on the 7th day and 14th day.The number of fibroblasts per unit area was significantly increased(P<0.01).The levels of IL-1β,IL-18 and TNF-α were significantly decreased(P<0.01).The expression levels of ASC,Pro-Caspase1,Caspase1,and NLRP3 in the wound tissues were decreased(P<0.01),while the expression levels of Beclin-1,LC3-Ⅱ,mTOR,p-mTOR,Akt and p-Akt were increased(P<0.01,P<0.05).Conclusion Chonghe soft extract can reduce inflammatory reaction,promote the generation of fibro,regulate the Akt/mTOR-mediated NLRP3 inflammasome inactivation,improve the level of autophagy in wound,and promote ulcer wound healing in diabetic rats.

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