1.Early outcomes of robot-assisted subxiphoid approach and intercostal approach for anterior mediastinal tumors: A retrospective cohort study
Weiqiang ZENG ; Haili DANG ; Lifei WANG ; Zhen PENG ; Xiangdou BAI ; Bing WANG ; Xiaoyang HE ; Dacheng JIN ; Yunjiu GOU
Chinese Journal of Clinical Thoracic and Cardiovascular Surgery 2026;33(03):369-375
Objective To compare the clinical outcomes of subxiphoid robot-assisted thoracoscopic surgery (SRATS) and intercostal robot-assisted thoracoscopic surgery (IRATS) in the treatment of anterior mediastinal tumors. Methods A retrospective analysis was conducted on patients with anterior mediastinal tumors who underwent robot-assisted surgery in the Department of Thoracic Surgery, Gansu Provincial Hospital, from May 2020 to July 2022. According to the surgical approach, patients were divided into an SRATS group and an IRATS group. Perioperative data were compared between the two groups. Results A total of 87 patients were included. There were 41 patients in the SRATS group [23 males, 18 females; mean age, (44.51±11.28) years] and 46 patients in the IRATS group [21 males, 25 females; mean age, (46.67±8.76) years]. Compared with the IRATS group, the SRATS group had significantly less intraoperative blood loss [(24.41±6.67) mL vs. (37.93±9.23) mL, P<0.001], shorter postoperative drainage duration [(1.73±0.59) days vs. (2.54±0.50) days, P<0.001], lower postoperative drainage volume [(94.46±34.08) mLvs. (116.72±24.90) mL, P=0.001], lower visual analogue scale (VAS) pain scores on postoperative day 1 [(3.66±0.76) points vs. (4.15±0.84) points, P=0.005] and day 3 [(2.41±0.59) points vs. (2.89±0.82) points, P=0.003], shorter postoperative hospital stay [(4.12±0.81) days vs. (4.98±1.02) days, P<0.001], and lower hospitalization costs [(4.51±0.65) ten thousand yuan vs. (4.86±0.68) ten thousand yuan, P=0.020]. There were no statistical differences between the two groups in operative time or incidence of postoperative complications (P>0.05). Conclusion Both SRATS and IRATS are safe and effective for the treatment of anterior mediastinal tumors. However, SRATS is less invasive and more conducive to enhanced postoperative recovery.
2.Herbal Textual Research on Patriniae Herba in Famous Classical Formulas
Yu SHI ; Zhen ZENG ; Feng ZHOU ; Yihan WANG ; Yanmeng LIU ; Yang YANG ; Zhilai ZHAN
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(10):248-257
By consulting ancient and modern literature, this article systematically reviews and verifies the historical evolution of the herbal medicine known as Baijiang across various dimensions, including name, origin, scientific name verification, medicinal parts, production area, quality, harvesting and processing, as well as its nature, taste, and therapeutic effects, in order to provide a reference for the development and utilization of famous classical formulas containing Patriniae Herba. Patriniae Herba has a long history of use. It derives its name from the distinctive musty odor of its roots, which resembles spoiled soy sauce. However, due to its alias Kucai, there has been much confusion with other plants. Since the Ming dynasty, various plants have been used interchangeably as Baijiang. Herbal textual research showed that Patriniae Herba was first recorded in Shennong Bencaojing, and throughout history, Baijiang has been recognized as its standard name, though it has also been known by alternative names such as Luchang, Lujiang, and Suanyi. The main sources used throughout the ages were Patrinia scabiosaefolia or P. villosa, which is consistent with the 1977 edition of the Pharmacopoeia of the People's Republic of China. However, while the roots were traditionally used medicinally, the whole plant is now more commonly used in modern practice. In addition, the whole plants of Thlaspi arvense from the Cruciferae family and Sonchus brachyotus from the Compositae family are commonly used as regional substitutes for Baijiang. According to ancient records, Patriniae Herba was primarily found in Jiangxia(present-day eastern Hubei province) and Jiangdong(the region south of the lower reaches of the Yangtze River), but modern literature shows that it is distributed throughout the country without a distinct geographical origin. In ancient times, the roots were harvested in August and sun-dried, today, the whole plant is typically dug up in summer or autumn and sun-dried. In recent times, the quality has been summarized as being best when the roots are long, the leaves are abundant and green, and the aroma is strong. Regarding the processing, ancient methods often involved baking(drying over fire), while modern methods typically involve removing impurities, washing, and then cutting and drying the segments. The effects of Patriniae Herba are to clear heat and detoxify, eliminate blood stasis and drain pus. During the Han and Northern and Southern dynasties, it was used to treat skin diseases caused by heat, abscesses, postpartum diseases, and rheumatism, during the Five dynasties period, its therapeutic applications expanded to include diseases of the five senses, and by the modern era, conditions such as neurasthenia and insomnia were added. Regarding its properties and taste, it was recorded as bitter and neutral during the Han dynasty. By the Tang dynasty, it was slightly cold, with a taste of acrid and bitter. During the Yuan and Ming dynasties, it was mostly slightly cold and neutral, with a bitter and salty taste. In the Qing dynasty and modern times, it was mostly bitter and neutral, and in contemporary times, it has evolved to a taste of acrid, bitter, and cool. Based on the results of this study, it is recommended that when developing and utilizing famous classical formulas containing Patriniae Herba, one should select the entire herb of the historically mainstream sources, P. scabiosaefolia or P. villosa from the Valerianaceae family, and choose the processing method according to the prescription requirements. It is recommended to use raw products without specific requirements.
3.Herbal Textual Research on Patriniae Herba in Famous Classical Formulas
Yu SHI ; Zhen ZENG ; Feng ZHOU ; Yihan WANG ; Yanmeng LIU ; Yang YANG ; Zhilai ZHAN
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(10):248-257
By consulting ancient and modern literature, this article systematically reviews and verifies the historical evolution of the herbal medicine known as Baijiang across various dimensions, including name, origin, scientific name verification, medicinal parts, production area, quality, harvesting and processing, as well as its nature, taste, and therapeutic effects, in order to provide a reference for the development and utilization of famous classical formulas containing Patriniae Herba. Patriniae Herba has a long history of use. It derives its name from the distinctive musty odor of its roots, which resembles spoiled soy sauce. However, due to its alias Kucai, there has been much confusion with other plants. Since the Ming dynasty, various plants have been used interchangeably as Baijiang. Herbal textual research showed that Patriniae Herba was first recorded in Shennong Bencaojing, and throughout history, Baijiang has been recognized as its standard name, though it has also been known by alternative names such as Luchang, Lujiang, and Suanyi. The main sources used throughout the ages were Patrinia scabiosaefolia or P. villosa, which is consistent with the 1977 edition of the Pharmacopoeia of the People's Republic of China. However, while the roots were traditionally used medicinally, the whole plant is now more commonly used in modern practice. In addition, the whole plants of Thlaspi arvense from the Cruciferae family and Sonchus brachyotus from the Compositae family are commonly used as regional substitutes for Baijiang. According to ancient records, Patriniae Herba was primarily found in Jiangxia(present-day eastern Hubei province) and Jiangdong(the region south of the lower reaches of the Yangtze River), but modern literature shows that it is distributed throughout the country without a distinct geographical origin. In ancient times, the roots were harvested in August and sun-dried, today, the whole plant is typically dug up in summer or autumn and sun-dried. In recent times, the quality has been summarized as being best when the roots are long, the leaves are abundant and green, and the aroma is strong. Regarding the processing, ancient methods often involved baking(drying over fire), while modern methods typically involve removing impurities, washing, and then cutting and drying the segments. The effects of Patriniae Herba are to clear heat and detoxify, eliminate blood stasis and drain pus. During the Han and Northern and Southern dynasties, it was used to treat skin diseases caused by heat, abscesses, postpartum diseases, and rheumatism, during the Five dynasties period, its therapeutic applications expanded to include diseases of the five senses, and by the modern era, conditions such as neurasthenia and insomnia were added. Regarding its properties and taste, it was recorded as bitter and neutral during the Han dynasty. By the Tang dynasty, it was slightly cold, with a taste of acrid and bitter. During the Yuan and Ming dynasties, it was mostly slightly cold and neutral, with a bitter and salty taste. In the Qing dynasty and modern times, it was mostly bitter and neutral, and in contemporary times, it has evolved to a taste of acrid, bitter, and cool. Based on the results of this study, it is recommended that when developing and utilizing famous classical formulas containing Patriniae Herba, one should select the entire herb of the historically mainstream sources, P. scabiosaefolia or P. villosa from the Valerianaceae family, and choose the processing method according to the prescription requirements. It is recommended to use raw products without specific requirements.
4.Effect and mechanism of beta-caryophyllene in mice with osteoarthritis
Ju CHEN ; Jinchang ZHENG ; Zhen LIANG ; Chengshuo HUANG ; Hao LIN ; Li ZENG
Chinese Journal of Tissue Engineering Research 2026;30(6):1341-1347
BACKGROUND:β-Caryophyllene has a variety of pharmacological activities such as antioxidant,anti-inflammatory and anti-apoptotic,which may have a better therapeutic effect on osteoarthritis.OBJECTIVE:To investigate the effect and mechanism of β-caryophyllene on mouse osteoarthritis.METHODS:Forty C57BL/6J mice were randomly divided into sham group,model group,low-dose β-caryophyllene group and high-dose β-caryophyllene group,with 10 mice in each group.Hulth method was used to construct an osteoarthritis model in the latter three groups.Four weeks after modeling,70 and 140 mg/kg/d β-caryophyllene was intragastrically given in the low-and high-dose β-caryophyllene groups,respectively,and normal saline was given by gavage in the sham group and the model group,once a day,for 4 weeks.After administration,knee joint morphological changes were observed by hematoxylin-eosin staining,serum levels of inflammatory factors(tumor necrosis factor-α,interleukin-1β,interleukin-6,and interleukin-10)were detected by ELISA,and oxidative stress indexes(glutathione peroxidase,superoxide dismutase,and malondialdehyde)were detected by chemiluminescence.The expression levels of key proteins in the Sonic hedgehog(Shh)/glioma associated oncogene homolog 1(Gli1)signaling pathway were detected by immunohistochemistry and western blot.RESULTS AND CONCLUSION:(1)Compared with the sham group,a large number of inflammatory cells infiltrated in the knee joint of mice in the model group,cartilage tissue was seriously damaged,serum levels of tumor necrosis factor-α,interleukin-1β,interleukin-6,interleukin-10 and malondialdehyde were significantly increased(P<0.01),the activities of glutathione peroxidase and superoxide dismutase were significantly decreased(P<0.01),and the relative expression levels of Shh and Gli1 in the knee joint were significantly increased(P<0.01).(2)Compared with the model group,in the low-and high-dose β-caryophyllene groups,inflammatory cell infiltration in the mouse knee joint was decreased,cartilage tissue injury was alleviated,serum levels of tumor necrosis factor-α,interleukin-1 β,interleukin-6 and malondialdehyde were significantly decreased(P<0.05),the activities of glutathione peroxidase and superoxide dismutase were significantly increased(P<0.01),and the expression levels of Shh and Gli1 in the knee joint were significantly decreased(P<0.01).The above-mentioned improvements were more significant in the high-dose β-caryophyllene group than the low-dose β-caryophyllene group.To conclude,β-caryophyllene can improve osteoarthritis,and its mechanism may be related to reducing inflammation and oxidative stress damage by regulating the Shh/Gli1 signaling pathway.
5.Effect and mechanism of beta-caryophyllene in mice with osteoarthritis
Ju CHEN ; Jinchang ZHENG ; Zhen LIANG ; Chengshuo HUANG ; Hao LIN ; Li ZENG
Chinese Journal of Tissue Engineering Research 2026;30(6):1341-1347
BACKGROUND:β-Caryophyllene has a variety of pharmacological activities such as antioxidant,anti-inflammatory and anti-apoptotic,which may have a better therapeutic effect on osteoarthritis.OBJECTIVE:To investigate the effect and mechanism of β-caryophyllene on mouse osteoarthritis.METHODS:Forty C57BL/6J mice were randomly divided into sham group,model group,low-dose β-caryophyllene group and high-dose β-caryophyllene group,with 10 mice in each group.Hulth method was used to construct an osteoarthritis model in the latter three groups.Four weeks after modeling,70 and 140 mg/kg/d β-caryophyllene was intragastrically given in the low-and high-dose β-caryophyllene groups,respectively,and normal saline was given by gavage in the sham group and the model group,once a day,for 4 weeks.After administration,knee joint morphological changes were observed by hematoxylin-eosin staining,serum levels of inflammatory factors(tumor necrosis factor-α,interleukin-1β,interleukin-6,and interleukin-10)were detected by ELISA,and oxidative stress indexes(glutathione peroxidase,superoxide dismutase,and malondialdehyde)were detected by chemiluminescence.The expression levels of key proteins in the Sonic hedgehog(Shh)/glioma associated oncogene homolog 1(Gli1)signaling pathway were detected by immunohistochemistry and western blot.RESULTS AND CONCLUSION:(1)Compared with the sham group,a large number of inflammatory cells infiltrated in the knee joint of mice in the model group,cartilage tissue was seriously damaged,serum levels of tumor necrosis factor-α,interleukin-1β,interleukin-6,interleukin-10 and malondialdehyde were significantly increased(P<0.01),the activities of glutathione peroxidase and superoxide dismutase were significantly decreased(P<0.01),and the relative expression levels of Shh and Gli1 in the knee joint were significantly increased(P<0.01).(2)Compared with the model group,in the low-and high-dose β-caryophyllene groups,inflammatory cell infiltration in the mouse knee joint was decreased,cartilage tissue injury was alleviated,serum levels of tumor necrosis factor-α,interleukin-1 β,interleukin-6 and malondialdehyde were significantly decreased(P<0.05),the activities of glutathione peroxidase and superoxide dismutase were significantly increased(P<0.01),and the expression levels of Shh and Gli1 in the knee joint were significantly decreased(P<0.01).The above-mentioned improvements were more significant in the high-dose β-caryophyllene group than the low-dose β-caryophyllene group.To conclude,β-caryophyllene can improve osteoarthritis,and its mechanism may be related to reducing inflammation and oxidative stress damage by regulating the Shh/Gli1 signaling pathway.
6.Survey of post-discharge exercise behavior and analysis of factors influencing exercise intensity in patients undergoing lung surgery
Hongyu ZENG ; Xiang WANG ; Tian ZHANG ; Yaqin WANG ; Xing WEI ; Zhen DAI ; Liping ZHANG ; Xiaoqin LIU ; Qiang LI ; Qiuling SHI ; Wei DAI ; Jia LIAO
Chinese Journal of Clinical Thoracic and Cardiovascular Surgery 2026;33(05):734-742
Objective To investigate the post-discharge exercise behavior and factors influencing moderate to vigorous intensity physical activity (MVPA) in patients undergoing lung surgery. Methods A total of 2874 patients from the large prospective, observational perioperative lung symptom study cohort (CN-PRO-Lung 3) in the Department of Thoracic Surgery at Sichuan Cancer Hospital between April 7, 2021, and January 31, 2024, were selected as the survey subjects. A survey was conducted using the Investigation of Exercise Behavior after Lung Surgery questionnaire and the International Physical Activity Questionnaire-Short Form (IPAQ-SF) among patients who underwent lung surgery. Binary logistic regression was used to analyze the factors influencing patients’ engagement in MVPA. Results A total of 702 patients were surveyed, including 252 males and 450 females, with an average age of (52.4±10.2) years. Patients with lung cancer accounted for 85.9%. Only 36.0% of the patients had regular exercise habits, while 42.3% did not engage in any physical activity. The three main barriers for postoperative exercise were physical discomfort (pain, coughing, shortness of breath, etc, 54.7%), lack of professional guidance (41.7%), and concerns about the surgical wound (28.9%). The proportions of patients engaging in vigorous, moderate, and low-intensity physical activity were 5.7%, 28.2%, and 66.1%, respectively. Multivariate analysis showed that patients with a personal annual income ≥50000 yuan (OR=1.52, 95%CI 1.01-2.29, P=0.044), high school education or above (OR=1.92, 95%CI 1.33-2.76, P<0.001), and lobectomy (OR=1.44, 95%CI 1.02-2.03, P=0.037) engaged in more MVPA. Conclusion Patients undergoing lung surgery have inadequate physical activity after discharge, particularly lacking in MVPA. Patients with higher income, higher educational levels, and lobectomy are more frequently engaged in MVPA. Measures such as symptom control, providing exercise guidance, and enhancing education on wound care may potentially improve the inadequate physical activity in lung surgery patients after discharge.
7.Fast Screening of 10 Kinds of Illegal Aphrodisiac Drugs in Foods by Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry
Xi ZENG ; Yu WANG ; Ying-Li CHEN ; Tian-Tian ZHAO ; Zhen-Lin XU ; Heng-Xin ZHOU
Chinese Journal of Analytical Chemistry 2025;53(3):441-450,中插3-中插5
A matrix-assisted laser desorption ionization time-of-flight mass spectrometry(MALDI-TOF MS)method was developed for simultaneous analysis of 10 kinds of aphrodisiac drugs,including sildenafil,acetildenafil,nor-acetildenafil,homosildenafil,lodenafil carbonate,sildlenafil dimer impurity,vardenafil dimer,hydroxyacetildenafil,N-desmethylsildenafil and udenafil.By using different matrices(α-cyano-4-hydroxycinnamic acid(HCCA)and sinapic acid(SA)),the effects of solvents,amount of matrices,laser intensity and spotting methods on the peak strength and signal intensity of MALDI-TOF MS for the aphrodisiac drugs were investigated.As a result,SA was chosen as the matrix,and then dispersed in methanol-water(50∶50,V/V),and spotted by matrix firstly and sample secondly approach with the reflect linear positive mode and laser power of 60%.Under optimal conditions,the proposed MALDI-TOF MS method could obtain stable signal,high intensity and well-repeated mass spectrometric results.The results of method validation showed a linear range from 10 to 100 ng/mL,and the regression coefficients(r)were all above 0.985.The limits of detection(LOD)were 0.1-1.0 ng/mL,and the recoveries were in the range of 72.9%-109.9%for health wine,soft capsule and instant coffee samples,while the relative standard deviations(RSDs)ranged from 0.7%to 11.3%(n=3).The test results of 10 kinds of aphrodisiac drugs by MALDI-TOF MS were in accordance with the results of high-performance liquid chromatography-tandem mass spectrometry.This method exhibited high sensitivity,high accuracy,good anti-interference ability,low chemical solvents consumption and environmentally friendliness,and could be used to detect drugs without standards.The developed MALDI-TOF MS method could realize the non-target screening and detection of 10 kinds of illegally added aphrodisiac drugs in foods.
8.Intravascular volume in children with primary nephrotic syndrome using fractional excretion of filtered sodium
Juan LIANG ; Yafei ZHUANG ; Jin CHENG ; Shujuan ZHEN ; Yuheng LIANG ; Ping ZENG ; Hu SHAO ; Fengjun GUAN
International Journal of Laboratory Medicine 2025;46(15):1820-1824,1830
Objective To evaluate the intravascular volume at different levels of edema and disease course by the fractional excretion of filtered sodium(FeNa)of children with primary nephrotic syndrome(PNS).Methods A total of 172 children with newly diagnosed PNS who were hospitalized in the Affiliated Hospital of Xuzhou Medical University from September 2022 to September 2024 were selected and divided into non-e-dema group(n=51),mild edema group(n=43),moderate edema group(n=46)and severe edema group(n=32)according to the degree of edema at the time of admission.A total of 40 healthy children who underwent physical examination during the same period were selected as the healthy control group.Serum creatinine,ser-um sodium were detected before and after treatment.Urine samples were collected to detect urine creatinine,urine sodium,FeNa was calculated and compared according to the results,and the degree of edema was recor-ded.24 h urine samples were collected on the same day to detect 24 h urine protein quantification and 24 h u-rine volume.Results On day 1 to 2 of the course of the disease,about 12%of the PNS children had FeNa<0.2%,indicating insufficient intravascular volume,which was mainly concentrated in the severe edema group.The moderate,severe edema group had a significantly lower FeNa level than the non-edema group,mild edema group,and healthy control group(P<0.01).The moderate edema group had a significant increase in FeNa on days 6 to 7 of the course of the disease,and the severe edema group had a significant increase in Fena on days 11 to 12 of the course of the disease(P<0.01).Conclusion Intravascular volume of PNS children with mod-erate to severe edema is often reduced,and intravascular volume may be insufficient in severe edema.PNS chil-dren with moderate to severe edema have increased intravascular volume with the extension of the course of disease and the improvement of the condition.
9.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*
;
Gene Expression Regulation, Plant
;
Transcription Factors/chemistry*
;
Lonicera/classification*
;
Flowers/metabolism*
;
Phylogeny
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Gene Expression Profiling
;
Multigene Family
10.tRF Prospect: tRNA-derived Fragment Target Prediction Based on Neural Network Learning
Dai-Xi REN ; Jian-Yong YI ; Yong-Zhen MO ; Mei YANG ; Wei XIONG ; Zhao-Yang ZENG ; Lei SHI
Progress in Biochemistry and Biophysics 2025;52(9):2428-2438
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.

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