1.HyPepTox-Fuse: An interpretable hybrid framework for accurate peptide toxicity prediction fusing protein language model-based embeddings with conventional descriptors.
Duong Thanh TRAN ; Nhat Truong PHAM ; Nguyen Doan Hieu NGUYEN ; Leyi WEI ; Balachandran MANAVALAN
Journal of Pharmaceutical Analysis 2025;15(8):101410-101410
Peptide-based therapeutics hold great promise for the treatment of various diseases; however, their clinical application is often hindered by toxicity challenges. The accurate prediction of peptide toxicity is crucial for designing safe peptide-based therapeutics. While traditional experimental approaches are time-consuming and expensive, computational methods have emerged as viable alternatives, including similarity-based and machine learning (ML)-/deep learning (DL)-based methods. However, existing methods often struggle with robustness and generalizability. To address these challenges, we propose HyPepTox-Fuse, a novel framework that fuses protein language model (PLM)-based embeddings with conventional descriptors. HyPepTox-Fuse integrates ensemble PLM-based embeddings to achieve richer peptide representations by leveraging a cross-modal multi-head attention mechanism and Transformer architecture. A robust feature ranking and selection pipeline further refines conventional descriptors, thus enhancing prediction performance. Our framework outperforms state-of-the-art methods in cross-validation and independent evaluations, offering a scalable and reliable tool for peptide toxicity prediction. Moreover, we conducted a case study to validate the robustness and generalizability of HyPepTox-Fuse, highlighting its effectiveness in enhancing model performance. Furthermore, the HyPepTox-Fuse server is freely accessible at https://balalab-skku.org/HyPepTox-Fuse/ and the source code is publicly available at https://github.com/cbbl-skku-org/HyPepTox-Fuse/. The study thus presents an intuitive platform for predicting peptide toxicity and supports reproducibility through openly available datasets.
2.HyPepTox-Fuse:An interpretable hybrid framework for accurate peptide toxicity prediction fusing protein language model-based embeddings with conventional descriptors
Thanh-Tran DUONG ; Truong-Pham NHAT ; Leyi WEI ; Balachandran MANAVALAN
Journal of Pharmaceutical Analysis 2025;15(8):1873-1886
Peptide-based therapeutics hold great promise for the treatment of various diseases;however,their clinical application is often hindered by toxicity challenges.The accurate prediction of peptide toxicity is crucial for designing safe peptide-based therapeutics.While traditional experimental approaches are time-consuming and expensive,computational methods have emerged as viable alternatives,including similarity-based and machine learning(ML)-/deep learning(DL)-based methods.However,existing methods often struggle with robustness and generalizability.To address these challenges,we propose HyPepTox-Fuse,a novel framework that fuses protein language model(PLM)-based embeddings with conventional descriptors.HyPepTox-Fuse integrates ensemble PLM-based embeddings to achieve richer peptide representations by leveraging a cross-modal multi-head attention mechanism and Transformer architecture.A robust feature ranking and selection pipeline further refines conventional descriptors,thus enhancing prediction performance.Our framework outperforms state-of-the-art methods in cross-validation and independent evaluations,offering a scalable and reliable tool for peptide toxicity pre-diction.Moreover,we conducted a case study to validate the robustness and generalizability of HyPepTox-Fuse,highlighting its effectiveness in enhancing model performance.Furthermore,the HyPepTox-Fuse server is freely accessible at https://balalab-skku.org/HyPepTox-Fuse/and the source code is publicly available at https://github.com/cbbl-skku-org/HyPepTox-Fuse/.The study thus presents an intuitive platform for predicting peptide toxicity and supports reproducibility through openly available datasets.
3.Saponins from the Leaves of Panax vietnamensis Ha et Grushv. (Vietnamese ginseng) and Their Inhibitory Activities on α-Glucosidase
Hoang Khang LE ; Thanh Tung PHAN ; Thi Thuy Duong NGO ; Cong Luan TRAN ; Poul Erik HANSEN ; Quang Ton THAT
Natural Product Sciences 2024;30(4):237-243
Vietnam boasts a rich and diverse flora, with many endemic species. Among them, Ngoc Linh ginseng (Vietnamese ginseng; scientific name: Panax vietnamensis Ha et Grushv.), a high-value endemic ginseng species, has been recognized as a national treasure. While numerous studies have been conducted on its rhizomes and roots, research on its leaves remains limited. In this study, six compounds (1–6) were isolated from the methanol extract of the leaves of P. vietnamensis. Their structures were elucidated using ESI-MS, 1D and 2D NMR spectroscopic methods, and comparisons with known literature data. The identified compounds are: 12β,20(R),25-β trihydroxydammara-3-O-β-D-glucopyranoside (1); 12β,20(R),25-trihydroxydammara-3-O-β-D-glucopyranosyl- (1→2)-β-D-glucopyranoside (2); notoginsenoside SFt1 (3); ginsenoside Rh2 (4); ginsenoside Rg3 (5) and notoginsenoside L1 (6). Except for compound 3, which was isolated from the leaves for the first time, the other five compounds are reported from this species for the first time. The α-glucosidase inhibition assay of the pure isolated compounds revealed that compounds 1, 4, and 6 exhibited significant activities, with IC50 values of 133.5, 105.5, and 14.9, respectively. For comparison, the positive control, acarbose, had an IC50 value of 138.2 µM.
4.Saponins from the Leaves of Panax vietnamensis Ha et Grushv. (Vietnamese ginseng) and Their Inhibitory Activities on α-Glucosidase
Hoang Khang LE ; Thanh Tung PHAN ; Thi Thuy Duong NGO ; Cong Luan TRAN ; Poul Erik HANSEN ; Quang Ton THAT
Natural Product Sciences 2024;30(4):237-243
Vietnam boasts a rich and diverse flora, with many endemic species. Among them, Ngoc Linh ginseng (Vietnamese ginseng; scientific name: Panax vietnamensis Ha et Grushv.), a high-value endemic ginseng species, has been recognized as a national treasure. While numerous studies have been conducted on its rhizomes and roots, research on its leaves remains limited. In this study, six compounds (1–6) were isolated from the methanol extract of the leaves of P. vietnamensis. Their structures were elucidated using ESI-MS, 1D and 2D NMR spectroscopic methods, and comparisons with known literature data. The identified compounds are: 12β,20(R),25-β trihydroxydammara-3-O-β-D-glucopyranoside (1); 12β,20(R),25-trihydroxydammara-3-O-β-D-glucopyranosyl- (1→2)-β-D-glucopyranoside (2); notoginsenoside SFt1 (3); ginsenoside Rh2 (4); ginsenoside Rg3 (5) and notoginsenoside L1 (6). Except for compound 3, which was isolated from the leaves for the first time, the other five compounds are reported from this species for the first time. The α-glucosidase inhibition assay of the pure isolated compounds revealed that compounds 1, 4, and 6 exhibited significant activities, with IC50 values of 133.5, 105.5, and 14.9, respectively. For comparison, the positive control, acarbose, had an IC50 value of 138.2 µM.
5.Saponins from the Leaves of Panax vietnamensis Ha et Grushv. (Vietnamese ginseng) and Their Inhibitory Activities on α-Glucosidase
Hoang Khang LE ; Thanh Tung PHAN ; Thi Thuy Duong NGO ; Cong Luan TRAN ; Poul Erik HANSEN ; Quang Ton THAT
Natural Product Sciences 2024;30(4):237-243
Vietnam boasts a rich and diverse flora, with many endemic species. Among them, Ngoc Linh ginseng (Vietnamese ginseng; scientific name: Panax vietnamensis Ha et Grushv.), a high-value endemic ginseng species, has been recognized as a national treasure. While numerous studies have been conducted on its rhizomes and roots, research on its leaves remains limited. In this study, six compounds (1–6) were isolated from the methanol extract of the leaves of P. vietnamensis. Their structures were elucidated using ESI-MS, 1D and 2D NMR spectroscopic methods, and comparisons with known literature data. The identified compounds are: 12β,20(R),25-β trihydroxydammara-3-O-β-D-glucopyranoside (1); 12β,20(R),25-trihydroxydammara-3-O-β-D-glucopyranosyl- (1→2)-β-D-glucopyranoside (2); notoginsenoside SFt1 (3); ginsenoside Rh2 (4); ginsenoside Rg3 (5) and notoginsenoside L1 (6). Except for compound 3, which was isolated from the leaves for the first time, the other five compounds are reported from this species for the first time. The α-glucosidase inhibition assay of the pure isolated compounds revealed that compounds 1, 4, and 6 exhibited significant activities, with IC50 values of 133.5, 105.5, and 14.9, respectively. For comparison, the positive control, acarbose, had an IC50 value of 138.2 µM.
6.Saponins from the Leaves of Panax vietnamensis Ha et Grushv. (Vietnamese ginseng) and Their Inhibitory Activities on α-Glucosidase
Hoang Khang LE ; Thanh Tung PHAN ; Thi Thuy Duong NGO ; Cong Luan TRAN ; Poul Erik HANSEN ; Quang Ton THAT
Natural Product Sciences 2024;30(4):237-243
Vietnam boasts a rich and diverse flora, with many endemic species. Among them, Ngoc Linh ginseng (Vietnamese ginseng; scientific name: Panax vietnamensis Ha et Grushv.), a high-value endemic ginseng species, has been recognized as a national treasure. While numerous studies have been conducted on its rhizomes and roots, research on its leaves remains limited. In this study, six compounds (1–6) were isolated from the methanol extract of the leaves of P. vietnamensis. Their structures were elucidated using ESI-MS, 1D and 2D NMR spectroscopic methods, and comparisons with known literature data. The identified compounds are: 12β,20(R),25-β trihydroxydammara-3-O-β-D-glucopyranoside (1); 12β,20(R),25-trihydroxydammara-3-O-β-D-glucopyranosyl- (1→2)-β-D-glucopyranoside (2); notoginsenoside SFt1 (3); ginsenoside Rh2 (4); ginsenoside Rg3 (5) and notoginsenoside L1 (6). Except for compound 3, which was isolated from the leaves for the first time, the other five compounds are reported from this species for the first time. The α-glucosidase inhibition assay of the pure isolated compounds revealed that compounds 1, 4, and 6 exhibited significant activities, with IC50 values of 133.5, 105.5, and 14.9, respectively. For comparison, the positive control, acarbose, had an IC50 value of 138.2 µM.
7.Within-household SARS-CoV-2 transmission and vaccine effectiveness in the first three COVID-19 school outbreaks in northern Viet Nam, September–December 2021
Trang Thu Vu ; Tu Huy Ngo ; Khanh Cong Nguyen ; Vu Thi Lan ; Cu Thi Bich Hanh ; Le Hong Son ; Huyen Thi Nguyen ; Hien Thi Nguyen ; Nghia Duy Ngu ; Duong Nhu Tran ; Duc-Anh Dang ; Florian Vogt ; Thai Quang Pham
Western Pacific Surveillance and Response 2024;15(3):19-30
Objective: The risk of transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from schoolchildren to their household and the protective effects of vaccination in these settings remain poorly understood. We assessed the transmission dynamics of schoolchildren with SARS-CoV-2 within their households and the protective effects of coronavirus disease (COVID-19) vaccination among household members in Viet Nam.
Methods: We estimated the attack rate, vaccine effectiveness and adjusted risk ratio (aRR) of factors associated with SARS-CoV-2 transmission to household contacts of children confirmed to have COVID-19 who attended three schools in Ha Nam, Phu Tho and Thanh Hoa provinces between September and December 2021 using multivariable regression with household-level random effects.
Results: This retrospective cohort study included 157 children infected with SARS-CoV-2 and their 540 household contacts. The attack rate among household contacts was 24.6% (133/540). Overall, vaccine effectiveness among household contacts was 39% (95% confidence interval [CI]: -1 to -63), higher among males than females and higher in adults aged >40 years. COVID-19 transmission was greater among female household contacts compared with males (aRR: 1.35, 95% CI: 0.94 to 1.95), although not statistically significant, and highest among those aged 19–39 years (aRR: 2.51, 95% CI: 1.50 to 4.21). Fully vaccinated household contacts had significantly lower infection risk (aRR: 0.46, 95% CI: 0.26 to 0.84).
Discussion: We found substantial onward transmission of SARS-CoV-2 from schoolchildren to household members, and older people were more likely to be protected by vaccination. We recommend that schoolchildren and all household members living with schoolchildren receive at least two doses of a COVID-19 vaccine. Recognizing the role of schoolchildren in the onward transmission of COVID-19 is an important lesson learned by Viet Nam that can help not only in managing other outbreaks but also in protecting schoolchildren by predicting the progress of the outbreak and preparing for a timely response.
8.Impact of long COVID-19 on posttraumatic stress disorderas modified by health literacy: an observational study inVietnam
Han Thi VO ; Tien Duc DAO ; Tuyen Van DUONG ; Tan Thanh NGUYEN ; Binh Nhu DO ; Tinh Xuan DO ; Khue Minh PHAM ; Vinh Hai VU ; Linh Van PHAM ; Lien Thi Hong NGUYEN ; Lan Thi Huong LE ; Hoang Cong NGUYEN ; Nga Hoang DANG ; Trung Huu NGUYEN ; Anh The NGUYEN ; Hoan Van NGUYEN ; Phuoc Ba NGUYEN ; Hoai Thi Thanh NGUYEN ; Thu Thi Minh PHAM ; Thuy Thi LE ; Thao Thi Phuong NGUYEN ; Cuong Quoc TRAN ; Kien Trung NGUYEN
Osong Public Health and Research Perspectives 2024;15(1):33-44
Objectives:
The prevalence of posttraumatic stress disorder (PTSD) has increased, particularly among individuals who have recovered from coronavirus disease 2019 (COVID-19) infection. Health literacy is considered a “social vaccine” that helps people respond effectively to the pandemic. We aimed to investigate the association between long COVID-19 and PTSD, and to examine the modifying role of health literacy in this association.
Methods:
A cross-sectional study was conducted at 18 hospitals and health centers in Vietnamfrom December 2021 to October 2022. We recruited 4,463 individuals who had recovered from COVID-19 infection for at least 4 weeks. Participants provided information about their sociodemographics, clinical parameters, health-related behaviors, health literacy (usingthe 12-item short-form health literacy scale), long COVID-19 symptoms and PTSD (Impact Event Scale-Revised score of 33 or higher). Logistic regression models were used to examine associations and interactions.
Results:
Out of the study sample, 55.9% had long COVID-19 symptoms, and 49.6% had PTSD.Individuals with long COVID-19 symptoms had a higher likelihood of PTSD (odds ratio [OR], 1.86; 95% confidence interval [CI], 1.63–2.12; p < 0.001). Higher health literacy was associated with a lower likelihood of PTSD (OR, 0.98; 95% CI, 0.97–0.99; p = 0.001). Compared to those without long COVID-19 symptoms and the lowest health literacy score, those with long COVID-19 symptoms and a 1-point health literacy increment had a 3% lower likelihood of PTSD (OR, 0.97; 95% CI, 0.96–0.99; p = 0.001).
Conclusion
Health literacy was found to be a protective factor against PTSD and modified the negative impact of long COVID-19 symptoms on PTSD.
9.Saponins from the Leaves of Panax vietnamensis Ha et Grushv. (Vietnamese ginseng) and Their Inhibitory Activities on α-Glucosidase
Hoang Khang LE ; Thanh Tung PHAN ; Thi Thuy Duong NGO ; Cong Luan TRAN ; Poul Erik HANSEN ; Quang Ton THAT
Natural Product Sciences 2024;30(4):237-243
Vietnam boasts a rich and diverse flora, with many endemic species. Among them, Ngoc Linh ginseng (Vietnamese ginseng; scientific name: Panax vietnamensis Ha et Grushv.), a high-value endemic ginseng species, has been recognized as a national treasure. While numerous studies have been conducted on its rhizomes and roots, research on its leaves remains limited. In this study, six compounds (1–6) were isolated from the methanol extract of the leaves of P. vietnamensis. Their structures were elucidated using ESI-MS, 1D and 2D NMR spectroscopic methods, and comparisons with known literature data. The identified compounds are: 12β,20(R),25-β trihydroxydammara-3-O-β-D-glucopyranoside (1); 12β,20(R),25-trihydroxydammara-3-O-β-D-glucopyranosyl- (1→2)-β-D-glucopyranoside (2); notoginsenoside SFt1 (3); ginsenoside Rh2 (4); ginsenoside Rg3 (5) and notoginsenoside L1 (6). Except for compound 3, which was isolated from the leaves for the first time, the other five compounds are reported from this species for the first time. The α-glucosidase inhibition assay of the pure isolated compounds revealed that compounds 1, 4, and 6 exhibited significant activities, with IC50 values of 133.5, 105.5, and 14.9, respectively. For comparison, the positive control, acarbose, had an IC50 value of 138.2 µM.
10.Predictors of twin pregnancy in in vitro fertilization with intracytoplasmic sperm injection cycles with day 3 double embryo transfer
Duy Le NGUYEN ; Hieu Le-Trung HOANG ; Vu Ngoc-Anh HO ; Toan Duong PHAM ; Nam Thanh NGUYEN ; Van Thi-Thu TRAN ; Tuong Manh HO ; Lan Ngoc VUONG
Clinical and Experimental Reproductive Medicine 2024;51(1):69-74
Objective:
The purpose of this study was to identify factors associated with twin pregnancy following day 3 double embryo transfer (DET).
Methods:
This retrospective cohort study incorporated data from 16,972 day 3 DET cycles. The participants were women aged between 18 and 45 years who underwent in vitro fertilization with intracytoplasmic sperm injection (IVF/ICSI) at My Duc Assisted Reproduction Technique Unit (IVFMD), My Duc Hospital, located in Ho Chi Minh City, Vietnam.
Results:
Of the 16,972 day 3 DET cycles investigated, 8,812 (51.9%) resulted in pregnancy. Of these, 6,108 cycles led to clinical pregnancy, with 1,543 (25.3% of clinical pregnancies) being twin pregnancies. Factors associated with twin pregnancy included age under 35 years (odds ratio [OR], 1.5; 95% confidence interval [CI], 1.32 to 1.71; p<0.001) and cycles involving the transfer of at least one grade I embryo. Relative to the transfer of two grade III embryos, the risk of twin pregnancy was significantly elevated following the transfer of two grade I embryos (OR, 1.40; 95% CI, 1.16 to 1.69; p<0.001) or a combination of one grade I and one grade II embryo (OR, 1.27; 95% CI, 1.05 to 1.55; p=0.001).
Conclusion
By analyzing a large number of IVF/ICSI cycles, we identified several predictors of twin pregnancy. These findings can assist medical professionals in tailoring treatment strategies for couples with infertility.


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