1.Diagnosis of invasive encapsulated follicular variant papillary thyroid carcinoma by protein-based machine learning
Truong Phan-Xuan NGUYEN ; Minh-Khang LE ; Sittiruk ROYTRAKUL ; Shanop SHUANGSHOTI ; Nakarin KITKUMTHORN ; Somboon KEELAWAT
Journal of Pathology and Translational Medicine 2025;59(1):39-49
Background:
Although the criteria for follicular-pattern thyroid tumors are well-established, diagnosing these lesions remains challenging in some cases. In the recent World Health Organization Classification of Endocrine and Neuroendocrine Tumors (5th edition), the invasive encapsulated follicular variant of papillary thyroid carcinoma was reclassified as its own entity. It is crucial to differentiate this variant of papillary thyroid carcinoma from low-risk follicular pattern tumors due to their shared morphological characteristics. Proteomics holds significant promise for detecting and quantifying protein biomarkers. We investigated the potential value of a protein biomarker panel defined by machine learning for identifying the invasive encapsulated follicular variant of papillary thyroid carcinoma, initially using formalin- fixed paraffin-embedded samples.
Methods:
We developed a supervised machine-learning model and tested its performance using proteomics data from 46 thyroid tissue samples.
Results:
We applied a random forest classifier utilizing five protein biomarkers (ZEB1, NUP98, C2C2L, NPAP1, and KCNJ3). This classifier achieved areas under the curve (AUCs) of 1.00 and accuracy rates of 1.00 in training samples for distinguishing the invasive encapsulated follicular variant of papillary thyroid carcinoma from non-malignant samples. Additionally, we analyzed the performance of single-protein/gene receiver operating characteristic in differentiating the invasive encapsulated follicular variant of papillary thyroid carcinoma from others within The Cancer Genome Atlas projects, which yielded an AUC >0.5.
Conclusions
We demonstrated that integration of high-throughput proteomics with machine learning can effectively differentiate the invasive encapsulated follicular variant of papillary thyroid carcinoma from other follicular pattern thyroid tumors.
2.Diagnosis of invasive encapsulated follicular variant papillary thyroid carcinoma by protein-based machine learning
Truong Phan-Xuan NGUYEN ; Minh-Khang LE ; Sittiruk ROYTRAKUL ; Shanop SHUANGSHOTI ; Nakarin KITKUMTHORN ; Somboon KEELAWAT
Journal of Pathology and Translational Medicine 2025;59(1):39-49
Background:
Although the criteria for follicular-pattern thyroid tumors are well-established, diagnosing these lesions remains challenging in some cases. In the recent World Health Organization Classification of Endocrine and Neuroendocrine Tumors (5th edition), the invasive encapsulated follicular variant of papillary thyroid carcinoma was reclassified as its own entity. It is crucial to differentiate this variant of papillary thyroid carcinoma from low-risk follicular pattern tumors due to their shared morphological characteristics. Proteomics holds significant promise for detecting and quantifying protein biomarkers. We investigated the potential value of a protein biomarker panel defined by machine learning for identifying the invasive encapsulated follicular variant of papillary thyroid carcinoma, initially using formalin- fixed paraffin-embedded samples.
Methods:
We developed a supervised machine-learning model and tested its performance using proteomics data from 46 thyroid tissue samples.
Results:
We applied a random forest classifier utilizing five protein biomarkers (ZEB1, NUP98, C2C2L, NPAP1, and KCNJ3). This classifier achieved areas under the curve (AUCs) of 1.00 and accuracy rates of 1.00 in training samples for distinguishing the invasive encapsulated follicular variant of papillary thyroid carcinoma from non-malignant samples. Additionally, we analyzed the performance of single-protein/gene receiver operating characteristic in differentiating the invasive encapsulated follicular variant of papillary thyroid carcinoma from others within The Cancer Genome Atlas projects, which yielded an AUC >0.5.
Conclusions
We demonstrated that integration of high-throughput proteomics with machine learning can effectively differentiate the invasive encapsulated follicular variant of papillary thyroid carcinoma from other follicular pattern thyroid tumors.
3.Diagnosis of invasive encapsulated follicular variant papillary thyroid carcinoma by protein-based machine learning
Truong Phan-Xuan NGUYEN ; Minh-Khang LE ; Sittiruk ROYTRAKUL ; Shanop SHUANGSHOTI ; Nakarin KITKUMTHORN ; Somboon KEELAWAT
Journal of Pathology and Translational Medicine 2025;59(1):39-49
Background:
Although the criteria for follicular-pattern thyroid tumors are well-established, diagnosing these lesions remains challenging in some cases. In the recent World Health Organization Classification of Endocrine and Neuroendocrine Tumors (5th edition), the invasive encapsulated follicular variant of papillary thyroid carcinoma was reclassified as its own entity. It is crucial to differentiate this variant of papillary thyroid carcinoma from low-risk follicular pattern tumors due to their shared morphological characteristics. Proteomics holds significant promise for detecting and quantifying protein biomarkers. We investigated the potential value of a protein biomarker panel defined by machine learning for identifying the invasive encapsulated follicular variant of papillary thyroid carcinoma, initially using formalin- fixed paraffin-embedded samples.
Methods:
We developed a supervised machine-learning model and tested its performance using proteomics data from 46 thyroid tissue samples.
Results:
We applied a random forest classifier utilizing five protein biomarkers (ZEB1, NUP98, C2C2L, NPAP1, and KCNJ3). This classifier achieved areas under the curve (AUCs) of 1.00 and accuracy rates of 1.00 in training samples for distinguishing the invasive encapsulated follicular variant of papillary thyroid carcinoma from non-malignant samples. Additionally, we analyzed the performance of single-protein/gene receiver operating characteristic in differentiating the invasive encapsulated follicular variant of papillary thyroid carcinoma from others within The Cancer Genome Atlas projects, which yielded an AUC >0.5.
Conclusions
We demonstrated that integration of high-throughput proteomics with machine learning can effectively differentiate the invasive encapsulated follicular variant of papillary thyroid carcinoma from other follicular pattern thyroid tumors.
4.Prevalence, multidrug resistance, and biofilm formation of Vibrio parahaemolyticus isolated from fish mariculture environments in Cat Ba Island, Vietnam
Kim Cuc Thi NGUYEN ; Phuc Hung TRUONG ; Hoa Truong THI ; Xuan Tuy HO ; Phu Van NGUYEN
Osong Public Health and Research Perspectives 2024;15(1):56-57
Objectives:
Vibrio parahaemolyticus is a major foodborne pathogen in aquatic animals and a threat to human health worldwide. This study investigated the prevalence, antimicrobial resistance, antimicrobial resistance genes (ARGs), and biofilm formation of V. parahaemolyticus strains isolated from fish mariculture environments in Cat Ba Island, Vietnam.
Methods:
In total, 150 rearing water samples were collected from 10 fish mariculture farms in winter and summer. A polymerase chain reaction assay was used to identify V. parahaemolyticus, its virulence factors, and ARGs. The antimicrobial resistance patterns and biofilm formation ability of V. parahaemolyticus strains were investigated using the disk diffusion test and a microtiter plate-based crystal violet method, respectively.
Results:
Thirty-seven V. parahaemolyticus isolates were recovered from 150 samples. The frequencies of the tdh and trh genes among V. parahaemolyticus isolates were 8.1% and 21.6%, respectively. More than 90% of isolates were susceptible to ceftazidime, cefotaxime, and chloramphenicol, but over 72% were resistant to ampicillin, tetracycline, and erythromycin. Furthermore, 67.57% of isolates exhibited multidrug resistance. The presence of ARGs related to gentamicin (aac(3)-IV), tetracycline (tetA) and ciprofloxacin (qnrA) in V. parahaemolyticus isolates was identified. Conversely, no ARGs related to ampicillin or erythromycin resistance were detected. Biofilm formation capacity was detected in significantly more multidrug-resistant isolates (64.9%) than non-multidrug-resistant isolates (18.9%).
Conclusion
Mariculture environments are a potential source of antibiotic-resistant V.parahaemolyticus and a hotspot for virulence genes and ARGs diffusing to aquatic environments. Thus, the prevention of antibiotic-resistant foodborne vibriosis in aquatic animals and humans requires continuous monitoring.
5.Knowledge, attitude and practice on the use of vietnamese medicinal plants for common diseases treatment among people in Phu Vang district, Thua Thien Hue province
Van Hung NGUYEN ; Thi Cam Quy TRUONG ; Xuan Vu NGUYEN ; Duc Hieu NGUYEN ; Thi Vui HUYNH ; Thi Ha Nhi TANG ; Thi Ngoc Giao LE ; Thanh Tu TRUONG ; Dinh Tuyen HOANG ; Dinh Hue LE
Hue Journal of Medicine and Pharmacy 2023;13(7):75-82
Background: Vietnamese herbs are considered as a botanical resource, a precious medicinal source of our country, and are widely used in the residential community in general. Phu Vang district is a coastal plain and lagoon in Thua Thien Hue province, where people’s living standards are not high, health facilities lack equipment. Therefore, the needs for primary health care are necessary to be strengthened, especially in the treatment of common diseases using Vietnamese herbs to reduce costs and improve health for the people. However, the knowledge of the local residents about Vietnamese herbs preventing and treating common diseases at home has not been surveyed. Objectives: (1) To describe the knowledge, attitude and practice on the use of Vietnamese herbs used in the treatment of common diseases of residents in some communes of Phu Vang district. (2) To determine some factors related to the use of Vietnamese herbs in the treatment of common diseases among the residents. Methods: A cross-sectional study was conducted on 400 residents representing the heads of households in three communes of Phu Vang district, Thua Thien Hue province, Thua Thien Hue province. Descriptive statistical analysis and multivariable logistic regression were performed with SPSS software. Results: Knowledge: Good: 45.2%; Fair: 30.8%; Average: 9.0%; Poor: 2.0%. Attitude: 97.0% of residents preferred using Vietnamese herbs in the treatment of common diseases, and 96.6% of residents agreed to continue using Vietnamese herbs to treat similar diseases later. Practice: Good: 7.8%; Fair: 16.7%; Average: 25.3%; Poor: 50.2%. Receiving information about Vietnamese herbs and growing them at home gardens were two factors related to the use of Vietnamese herbs to treat common diseases (p < 0.05). Conclusion: The practice of using Vietnamese herbs to treat common diseases of the residents in Phu Vang district is still low, it is necessary to strengthen educational propaganda to raise the awareness and practice among residents on the prevention and treatment of diseases with Vietnamese herbs at home.
6.A New Dimeric Lignan from the Stems of Willughbeia edulis
Hai Xuan NGUYEN ; Truong Nhat VAN DO ; Tho Huu LE ; Phu Hoang DANG ; Mai Thanh THI NGUYEN ; Nhan Trung NGUYEN
Natural Product Sciences 2022;28(2):53-57
As part of our continued study on the chemical constituents of Willughbeia edulis stems, a new dimeric lignan named edulignan (1) was isolated from its EtOAc-soluble extract. Based on NMR spectroscopic interpretation, the planar structure of 1 has been suggested to have two 2-substituted 4-chromanone subunits with different stereochemical configurations. In addition, the MS/MS analysis of the products obtained by acidcatalyzed hydrolysis of 1 was supportive of its structure. Unfornatually, the new compound 1 did not show α-glucosidase inhibitory activity with an IC 50 value > 250 μM.
7.Viral load suppression and acquired HIV drug resistance in adults receiving antiretroviral therapy in Viet Nam: results from a nationally representative survey
Vu Quoc Dat ; Bui Duc Duong ; Do Thi Nhan ; Nguyen Huu Hai ; Nguyen Thi Lan Anh ; Huynh Hoang Khanh Thu ; Tran Ton ; Luong Que Anh ; Nguyen Tuan Nghia ; Nguyen Vu Thuong ; Khuu Van Nghia ; Tran Thi Minh Tam ; Tran Phuc Hau ; Nguyen Duy Phuc ; Vu Xuan Thinh ; Nguyen Tran Hien ; Truong Thi Xuan Lien ; Silvia Bertagnolio ; Nguyen Thi Thuy Van ; Masaya Kato
Western Pacific Surveillance and Response 2018;9(3):16-24
Objective:
The purpose of this survey was to estimate the prevalence of viral load (VL) suppression and emergence of HIV drug resistance (HIVDR) among individuals receiving antiretroviral therapy (ART) for 36 months or longer in Viet Nam using a nationally representative sampling method.
Methods:
The survey was conducted between May and August 2014 using a two-stage cluster design. Sixteen ART clinics were selected using probability proportional to proxy size sampling, and patients receiving ART for at least 36 months were consecutively enrolled. Epidemiological information and blood specimens were collected for HIV-1 VL and HIVDR testing; HIVDR was defined by the Stanford University HIVDR algorithm.
Results:
Overall, 365 eligible individuals were recruited with a mean age of 38.2 years; 68.4% were men. The mean time on ART was 75.5 months (95% confidence interval [CI]: 69.0–81.9 months), and 93.7% of the patients were receiving non-nucleoside reverse transcriptase inhibitor-based regimens. Of the 365 individuals, 345 (94.7%, 95% CI: 64.1–99.4%) had VL below 1000 copies/mL and 19 (4.6%, 95% CI: 2.8-–7.5) had HIVDR mutations.
Discussion
Our nationally representative survey found a high level of VL suppression and a low prevalence of HIVDR among individuals who received ART for at least 36 months in Viet Nam. Continued surveillance for HIVDR is important for evaluating and improving HIV programs.
8.Respiratory virus laboratory pandemic planning and surveillance in central Viet Nam, 2008–2010
Tran Thomas ; Chien Bui Trong ; Papadakis Georgina ; Druce Julian ; Birch Chris ; Chibo Doris ; An Truong Phuoc ; Trang Le Thi Kim ; Trieu Nguyen Bao ; Thuy Doan Thi Thanh ; Catton Mike ; Mai Trinh Xuan
Western Pacific Surveillance and Response 2012;3(3):49-56
Introduction: Laboratory capacity is needed in central Viet Nam to provide early warning to public health authorities of respiratory outbreaks of importance to human health, for example the outbreak of influenza A(H1N1) pandemic in 2009. Polymerase chain reaction (PCR) procedures established as part of a capacity-building process were used to conduct prospective respiratory surveillance in a region where few previous studies have been undertaken. Methods: Between October 2008 and September 2010, nose and throat swabs from adults and children (approximately 20 per week) presenting with an acute respiratory illness to the Ninh Hoa General Hospital were collected. Same-day PCR testing and result reporting for 13 respiratory viruses were carried out by locally trained scientists. Results: Of 2144 surveillance samples tested, 1235 (57.6%) were positive for at least one virus. The most common were influenza A strains (17.9%), with pandemic influenza A(H1N1) 2009 and seasonal H3N2 strain accounting for 52% and 43% of these, respectively. Other virus detections included: rhinovirus (12.4%), enterovirus (8.9%), influenza B (8.3%), adenovirus (5.3%), parainfluenza (4.7%), respiratory syncytial virus (RSV) (3.9%), human coronavirus (3.0%) and human metapneumovirus (0.3%). The detection rate was greatest in the 0–5 year age group. Viral co-infections were identified in 148 (6.9%) cases. Discussion: The outbreak in 2009 of the influenza A(H1N1) pandemic strain provided a practical test of the laboratory’s pandemic plan. This study shows that the availability of appropriate equipment and molecular-based testing can contribute to important individual and public health outcomes in geographical locations susceptible to emerging infections.
9.The efficacy of low dose GNRH agonist depot in combination with recombinant FSH for ovarian stimulation in in vitro fertilization
Hoi Xuan Nguyen ; Tien Viet Nguyen ; Duyet Truong Pham
Journal of Medical Research 2008;58(5):71-75
Background: Ovarian stimulation is an important process in IVF. Objectives:To assess the efficacy of low dose GnRH agonist depot in combination with recombinant FSH for ovarian stimulation in IVF and evaluate the clinical pregnancy rate of this protocol. Subject and method: A prospective study recruited 60 patients undergoing IVF. The patients was injected intramuscularly with a single dose of diphereline of 1.25 mg on cycle day 21-23. Then recombinant FSH was given subcutaneously on day 3. hCG was injected intramuscularly when at least one follicle reached 18 mm in diameter. Oocytes retrieval in 36 hours and embryo 2 transfer on day after oocytes retrieval. Results: Duration of stimulation was 10.8 \xb1 0.9, average number of oocytes was 3.3 \xb1 4.7, average number of embryos was 6.5 \xb1 4.1, clinical pregnancy rate was 41.7%. Ovarian hyperstimulation rate was 5%, frozen embryo rate was 40 %. Conclusions: The use of low dose GnRH agonist depot in combination with recombinant ISH is effective for ovarian stimulation in IVF.
In vitro Fertilization (IVF)
;
Ovarian stimulation
;
Oocytes retrieval
;
Embryo transfer
;
GnRH agonist
10.The preliminary report of occult HBV infection in Vietnamese
Truong Xuan Bui ; Bang Van Nguyen ; Phuong Minh Tran ; Trach Khanh Nguyen ; Quy Tran ; Yoshihiko Yano ; Yasushi Seo ; Yoshitake Hayashi
Journal of Medical Research 2007;47(1):28-32
Background: Vietnam is located in the endemic region of hepatitis B virus (HBV) infection, but no data of occult HBV infection was reported at present. Objectives: To investigate the prevalence of occult HBV infection in different ethnics of people and generations. Subjects and method: 80 voluteers with HbsAg negative from five different ethnics: Kinh, Tay, Mong, Giay and Dao in a Chino \ufffd?Vietnamses border province (Lao Cai) were enrolled in the study. After HBV-DNA was extracted, nested PCR of S gene and of Core-promoter/Pre-core region were used to detect HBV-DNA. Specifying nucleotide sequence was confirmed by direct sequencing. Results:The prevalence of occult HBV infection in population study was very high 73/80 (91,3%) by nested PCR of Core-promoter/Pre-core, significantly more sensitive than nested PCR of S gene (26,3%) (p<0,0001). The prevalence of occult HBV infection was notdifferent between ethnics of people or between children, adults. Conclusion: Occult HBV infection in Vietnamese is very common; however, nationwide further studies should be carried out to confirm this preliminary results and evaluate the impact of occult HBV infection in Vietnam.
Hepatitis B virus
;
Hepatitis B Surface Antigens
;


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