1.Research on The Genealogical Inference Efficiency of High-density SNPs
Jing LI ; Yi-Jie SUN ; Wen-Ting ZHAO ; Zi-Chen TANG ; Jing LIU ; Cai-Xia LI
Progress in Biochemistry and Biophysics 2026;53(3):740-753
ObjectiveThis study aims to explore the potential of different orders of magnitude single-nucleotide polymorphism (SNP) locus combinations for predicting distant kinship relationships. A high-density SNP locus set was constructed, and a comprehensive assessment of its inference capability was conducted. MethodsFirstly, we selected three commercial chip panels, CGA (Chinese genotyping array, Illumina), GSA (Global screening array, Illumina), Affy (23MF_V2 high-density SNP array, Affymetrix) and merged them after quality control, forming a high-density SNP locus panel(1 180 k). Secondly, we selected 161 samples and collected their peripheral blood samples by using whole-genome sequencing technology. Within this sample population, the levels of kinship relationships fully covered the range from level 1 to level 9, and the number of kinship pairs at each level was consistently maintained at over 50 pairs. From 161 samples data of whole-genome sequencing, the 1 180 k locus set was extracted, which is referred to as the high-density SNP locus set in the following text. The kinship inference was conducted using the identity-by-descent (IBD) algorithm with the selected optimal parameters. To comprehensively evaluate the performance of the high-density SNP locus set in kinship inference, we compared it with the three commercial chip panels, the intersection of these three chip loci, and the control sets constructed by randomly reducing the number of the high-density SNP locus set. Based on the changes in the IBD lengths, as well as the dynamic trends in prediction accuracy, we conducted a scientific assessment of the kinship inference capability of the high-density SNP locus set. ResultsAfter screening, a set of 1 184 334 autosomal SNPs was obtained. During the process of screening the optimal IBD length threshold, the result revealed that 0 cM, 1 cM, and 2 cM all demonstrated good applicability. However, to avoid the issue of a large amount of redundant information caused by setting a too low IBD length threshold, this study ultimately selected 2 cM as the optimal threshold. Compared with the average results of three chip panels, the high-density SNP locus set increased the total IBD length and the average IBD length across levels 1-9; the accuracy of the confidence interval for level 8 was 70.97%, which represented a 3.50% improvement; the average confidence interval accuracy for levels 1-8 was 91.39%, representing a 1.00% increase; and the false negative rates at levels 8 and 9 were reduced by 2.42% and 6.76%, respectively. The system efficacy of the high-density SNP locus set for kinship inference of first to eighth degree relationships reached 98.91%. Through random reduction of the high-density SNP locus set results, it is found that increasing the number of SNPs with the panel, the detection efficiency of IBD length showed a significant upward trend. At the same time, the overall trend in the accuracy of kinship relationship prediction as well as the confidence interval accuracy also indicated that both metrics steadily increased with the addition of more loci. ConclusionThe results show that the high-density SNPs panel significantly enhances the efficacy of distant kinship inference, accurately covering kinship degrees, with the average confidence interval accuracy for first to eighth degree relationships stably above 90%. The study finds that increasing the number of SNPs panel can improve the ability to predict distant kinship.
2.Pollution levels and health risk assessment of nitrosamines in pipeline direct drinking water from primary and secondary schools in Shanghai
Ting WANG ; Chaoye SHEN ; Zhe CHEN ; Jian CHEN ; Yi SU
Journal of Environmental and Occupational Medicine 2026;43(5):637-642
Background Nitrosamines (NAms), emerging as disinfection by-products in drinking water, are highly carcinogenic. Given the significant NAms contamination reported in various regions of China, evaluating the contamination levels and health risks of NAms in terminal direct drinking water is of great urgency. Objective To investigate the concentration levels of NAms in piped direct drinking water at primary and secondary schools in Shanghai, and to assess the potential health risks posed to different age groups through this exposure pathway. Methods A total of 198 water samples were collected from 66 primary and secondary schools across five districts in Shanghai from May to June 2023. The mass concentrations of eight major NAms were quantified using solid-phase extraction coupled with gas chromatography-mass spectrometry (GC-MS). A carcinogenic health risk model was employed to evaluate the lifetime cancer risks associated with NAms exposure via direct drinking water for various age groups. Results Among the 198 samples, NAms were detected in 196 samples, with concentrationsranging from below the limit of detection (LOD) to 106.06 ng·L−1. The average concentration of total NAms was 21.30 ng·L−1, with N-nitrosodimethylamine (NDMA) exhibiting the highest detection rate at 98.5%. Significant differences in NAms concentrations were observed among water treatment systems utilizing ultrafiltration (UF), nanofiltration (NF), and reverse osmosis (RO) as core processes (P<0.05). The lifetime cancer risks for different age groups ranged from 1.38×10−6 to 1.11×10−5, with NDMA contributing the most to the overall risk (82.1%). The carcinogenic risk for adults (1.08×10−5) was higher than that for children and adolescents (1.38×10−6 to 2.61×10−6). Among children and adolescents under 18 years of age, the risk decreased as age increased. Conclusion Trace levels of NAms, primarily NDMA, are detected in the piped direct drinking water at primary and secondary schools in Shanghai, with concentrations vary significantly depending on the water treatment process. The carcinogenic risks of NAms exposure via direct drinking water for all age groups are below the acceptable level (1×10−4) recommended by the U.S. Environmental Protection Agency (EPA).
3.Pollution levels and health risk assessment of nitrosamines in pipeline direct drinking water from primary and secondary schools in Shanghai
Ting WANG ; Chaoye SHEN ; Zhe CHEN ; Jian CHEN ; Yi SU
Journal of Environmental and Occupational Medicine 2026;43(5):637-642
Background Nitrosamines (NAms), emerging as disinfection by-products in drinking water, are highly carcinogenic. Given the significant NAms contamination reported in various regions of China, evaluating the contamination levels and health risks of NAms in terminal direct drinking water is of great urgency. Objective To investigate the concentration levels of NAms in piped direct drinking water at primary and secondary schools in Shanghai, and to assess the potential health risks posed to different age groups through this exposure pathway. Methods A total of 198 water samples were collected from 66 primary and secondary schools across five districts in Shanghai from May to June 2023. The mass concentrations of eight major NAms were quantified using solid-phase extraction coupled with gas chromatography-mass spectrometry (GC-MS). A carcinogenic health risk model was employed to evaluate the lifetime cancer risks associated with NAms exposure via direct drinking water for various age groups. Results Among the 198 samples, NAms were detected in 196 samples, with concentrationsranging from below the limit of detection (LOD) to 106.06 ng·L−1. The average concentration of total NAms was 21.30 ng·L−1, with N-nitrosodimethylamine (NDMA) exhibiting the highest detection rate at 98.5%. Significant differences in NAms concentrations were observed among water treatment systems utilizing ultrafiltration (UF), nanofiltration (NF), and reverse osmosis (RO) as core processes (P<0.05). The lifetime cancer risks for different age groups ranged from 1.38×10−6 to 1.11×10−5, with NDMA contributing the most to the overall risk (82.1%). The carcinogenic risk for adults (1.08×10−5) was higher than that for children and adolescents (1.38×10−6 to 2.61×10−6). Among children and adolescents under 18 years of age, the risk decreased as age increased. Conclusion Trace levels of NAms, primarily NDMA, are detected in the piped direct drinking water at primary and secondary schools in Shanghai, with concentrations vary significantly depending on the water treatment process. The carcinogenic risks of NAms exposure via direct drinking water for all age groups are below the acceptable level (1×10−4) recommended by the U.S. Environmental Protection Agency (EPA).
4.Effectiveness of primary tumor resection for survival after first-line cetuximab or bevacizumab in KRAS wild-type metastatic colorectal cancer treated with subsequent trifluridine/tipiracil or regorafenib
Yu-Hsun CHEN ; Chih-Chien WU ; Chien-Chou SU ; Pei-Ting LEE ; Yi-Chia SU
Annals of Coloproctology 2026;42(1):127-140
Purpose:
The optimal sequencing of targeted therapies and the role of primary tumor resection (PTR) in KRAS wild-type metastatic colorectal cancer (mCRC) remain unclear. This study compared survival outcomes in patients treated with first-line cetuximab plus FOLFIRI (folinic acid, 5-fluorouracil, and irinotecan) versus bevacizumab plus FOLFIRI, followed by second-line oxaliplatin-based chemotherapy and later-line trifluridine/tipiracil or regorafenib.
Methods:
This retrospective cohort study used Taiwan’s National Health Insurance Research Database and the Taiwan Cancer Registry. Patients diagnosed with mCRC between 2013 and 2019 were included if they received first-line cetuximab or bevacizumab plus FOLFIRI, followed by later-line trifluridine/tipiracil or regorafenib. Patients were stratified by PTR status. Primary endpoints were overall survival and survival during trifluridine/tipiracil or regorafenib treatment. Secondary endpoints included time to treatment discontinuation (TTD) and TTD during trifluridine/tipiracil or regorafenib therapy. Stabilized inverse probability of treatment weighting was used for adjustment.
Results:
Among 559 patients, 278 were assigned to the non-PTR group and 281 to the PTR group. In the non-PTR group, the cetuximab cohort demonstrated significantly longer survival during trifluridine/tipiracil or regorafenib therapy (6.2 months vs. 4.9 months; hazard ratio [HR], 0.72) and longer TTD1 (the interval between initiation of first-line therapy and the start of second-line chemotherapy; 11.8 months vs. 9.5 months; HR, 0.67) than the bevacizumab cohort. Survival differences between regimens were less pronounced among patients who underwent PTR.
Conclusion
First-line cetuximab plus FOLFIRI may confer a survival advantage over bevacizumab in patients with KRAS wild-type mCRC without PTR, including during later-line therapy with trifluridine/tipiracil or regorafenib, whereas bevacizumab appears to provide more consistent benefits in those with PTR.
5.Influence of atrial septal defect on mitral valve growth after repair of coarctation of the aorta or an interrupted aortic arch in infants
Yi-Chia WANG ; Heng-Wen CHOU ; Chi-Hsiang HUANG ; Hsing-Hao HUANG ; Yih-Sharng CHEN ; En-Ting WU ; Shyh-Jye CHEN ; Ming-Tai LIN ; Shuenn-Nan CHIU ; Shu-Chien HUANG
Clinical and Experimental Pediatrics 2026;69(4):322-329
Background:
Patients with coarctation of the aorta (CoA) and an interrupted aortic arch (IAA) may present with small mitral valves (MVs) and a reduced left ventricular (LV) volume. Biventricular repair (BVR) in these patients is dependent on adequate size of the left cardiac structures.Purpose: This study evaluated the impact of the hemodynamic characteristics of atrial septal defects (ASDs) on MV growth following surgical repair.
Methods:
We retrospectively reviewed the data of patients diagnosed with CoA or IAA between 2007 and 2024. The z score for MV size measured 6 months postoperatively (Z2) was compared with the preoperative MV size (Z1). The factors associated with MV growth were also studied.
Results:
A total of 161 patients with CoA or IAA were included. Transthoracic echocardiography was used to assess the MV and LV dimensions preoperatively and 6 months postoperatively. Of the cohort, 155 (96.3%) underwent initial BVR and 6 underwent single-ventricle palliation. MV z scores significantly increased following BVR (mean change: +0.45±1.35; P<0.001) but decreased after single-ventricle repair (-0.56±0.49, P=0.04). Multivariate analysis identified the initial MV z score and ASD pressure gradient as independent predictors of MV growth (R2=0.39).
Conclusion
Annular growth of the MV was not observed in patients who underwent single-ventricle palliation. In contrast, among patients who achieved BVR, those with a small preoperative MV annulus and low ASD pressure gradient demonstrated subsequent catch-up MV growth, suggesting that adequate left-sided preload is essential for MV development.
6.Harnessing Machine Learning for Personalized Care of Patients With Idiopathic Sudden Sensorineural Hearing Loss: A Multicenter Cohort Study
Yen-Ting GUO ; Ching-Ting TAN ; Chen-Chi WU ; Chun-Ying WANG ; Chein-Yu HUANG ; Tzu-Hsiang YANG ; Ting-Yi LEE ; Ting-Hua YANG ; Tien-Chen LIU ; Pey-Yu CHEN ; Pei-Hsuan LIN
Clinical and Experimental Otorhinolaryngology 2026;19(2):194-204
Objectives:
. Idiopathic sudden sensorineural hearing loss (ISSNHL) is a significant cause of hearing loss. Intratympanic steroid injection (ITSI) is commonly used as an initial or salvage treatment; however, the lack of a standardized treatment protocol has resulted in variability in clinical practice. In addition, no efficient prediction model currently exists to support personalized management. Therefore, this study aimed to develop tailored management strategies for ISSNHL using a machine-learning model.
Methods:
. This retrospective multicenter cohort study was conducted between January 2015 and December 2020, with data analysis performed between January 2021 and March 2024. Patients were selected based on the International Classification of Diseases, 10th Revision criteria for ISSNHL, along with relevant medication and procedure codes. Patients with pure-tone audiogram results not meeting ISSNHL criteria, better initial hearing in the affected ear, an identifiable etiology, no post-treatment audiogram, or delayed treatment (>6 weeks) were excluded. We included 770 patients diagnosed with ISSNHL who received ITSI. The primary outcome was the area under the receiver operating characteristic curve for prediction performance. Recovery status was determined using the last pure-tone audiogram. Modeling was conducted on the Quanta for Medical Care AI platform using five machine-learning algorithms and a nested cross-validation framework, in which feature selection and hyperparameter tuning were performed in the inner folds and model performance was evaluated in the outer folds.
Results:
. A random forest classifier outperformed the other models in predicting hearing outcomes, achieving an area under the receiver operating characteristic curve of 0.788. Time to ITSI was the most influential treatment-related factor, with ITSI administered within 10 days of hearing loss being associated with better outcomes. This model can be used to provide personalized prognostic estimates under different treatment protocols.
Conclusion
. The machine-learning-based prediction model facilitates personalized treatment strategies and timely treatment adjustments for ISSNHL, thereby optimizing the likelihood of complete recovery.
7.Therapeutic Effects of Theta Burst Stimulation on Cognition Following Brain Injury
Wan-Ting CHEN ; Yi-Wei YEH ; Shin-Chang KUO ; Yi-Chih SHIAO ; Chih-Chung HUANG ; Yi-Guang WANG ; Chun-Yen CHEN
Clinical Psychopharmacology and Neuroscience 2025;23(1):161-165
This case report explores the therapeutic potential of theta burst stimulation (TBS) for cognitive enhancement in individuals with brain injuries. The study presents a 38-year-old male suffering from an organic mental disorder attributed to a traumatic brain injury (TBI), who demonstrated notable cognitive improvements following an intensive TBS protocol targeting the left dorsal lateral prefrontal cortex. The treatment led to significant enhancements in impulse control, irritability, and verbal comprehension without adverse effects. Neuropsychological assessments and brain imaging post-intervention revealed improvements in short-term memory, abstract reasoning, list-generating fluency, and increased cerebral blood flow in the prefrontal cortex. These findings suggest that TBS, by promoting neural plasticity and reconfiguring neural networks, offers a promising avenue for cognitive rehabilitation in TBI patients. Further research is warranted to optimize TBS protocols and understand the mechanisms underlying its cognitive benefits.
8.Validity and Cost-Consequence Analysis of the Brief Version of the Montreal Cognitive Assessment for Discriminating Cognitive Impairment in a Community-Based Middle-Aged and Elderly Population.
Ting PANG ; Ya-Ping ZHANG ; Ren-Wei CHEN ; Ai-Ju MA ; Xiao-Yi YU ; Yi-Wen HUANG ; Yi-Chun LU ; Xin XU
Acta Academiae Medicinae Sinicae 2025;47(3):382-389
Objective To evaluate the reliability and validity and perform cost-consequence analysis of the brief version of the Montreal cognitive assessment(MoCA)for identifying cognitive impairment in a community-based population ≥50 years of age.Methods The internal consistency and retest reliability of the brief version of the MoCA were analyzed,and the area under the curve(AUC),sensitivity,and specificity were determined to discriminate mild cognitive impairment(MCI)and dementia with the clinical dementia rating(CDR)as the diagnostic criterion.The consistency between the brief version and the full version was analyzed by the Kappa test and the Bland-Altman method,and the number of individuals entering the diagnostic assessment and the overall assessment time were estimated and compared between the two versions.Results A total of 303 individuals were included in this study,of whom 192,94,and 17 had normal cognitive function,MCI,and dementia,respectively.The Cronbach's α and re-test coefficients of the brief version of MoCA were 0.754 and 0.711(P<0.001),respectively.The brief version showed the AUC,sensitivity,and specificity of 0.889,74.5%,and 93.8% for identifying MCI,and 0.994,100%,and 93.8% for identifying dementia,respectively.When the brief version of MoCA was used to identify 94 patients with MCI in 303 individuals,107 individuals required additional diagnostic assessment,with an overall assessment time of 142.4 h,which represented decreases of 21.3% and 32.7%,respectively,compared with those of the full version.When the brief version of MoCA was used to identify 17 patients with dementia in 303 individuals,35 individuals required additional diagnostic assessment,with an overall assessment time of 70.4 h,a decrease of 29.5% in the time cost compared with the full version.Conclusions The brief version of MoCA can identify cognitively impaired individuals in a community-based middle-aged and elderly population,with diagnostic validity comparable to that of the full version but less time cost and fewer individuals needing additional diagnostic assessment to detect true-positive cases.It could be expanded for use in the community-based primary screening setting.
Humans
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Aged
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Middle Aged
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Cognitive Dysfunction/diagnosis*
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Male
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Female
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Mental Status and Dementia Tests
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Reproducibility of Results
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Dementia/diagnosis*
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Sensitivity and Specificity
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Aged, 80 and over
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Cost-Benefit Analysis
9.The protective effect of Gualou Guizhi granules on neuronal injury induced by LPS-activated microglia based on Notch signaling pathway
Xue-zhen LI ; Xiao-xue ZOU ; Wen-ting CHEN ; Yi FENG ; Ya-nan LI ; Yu-qin ZHANG ; Li-hong NAN
Chinese Pharmacological Bulletin 2025;41(4):781-786
Aim To investigate the protective effect of Gualou Guizhi granules(GLGZG)on neuronal injury induced by LPS-activated microglia based on Notch signaling pathway.Methods LPS-activated microglia were co-cultured with neurons to construct neuron inju-ry models,and the cells were divided into the control group,model group,Notch inhibitor(DAPT)group,GLGZG(50,100,200 mg·L-1)group,DAPT+100 mg·L-1GLGZG group.After intervention,the activity of HT22 cells was detected by CCK-8 method,and rel-ative mRNA expression was detected by real-time PCR.The relative protein expression was detected by Western blot.Results Compared with the model group,after GLGZG intervention,the cell activity was significantly improved,GLGZG decreased IL-6,IL-12,Bax,Notch 1,caspase-3,Delta-1,NICD,RBPSUH,HES1 expression,and increased Bcl-2 expression(P<0.05).Compared with the model group,the NICD,RBPSUH and HES1 mRNA and protein expressions significantly decreased after DAPT treatment(P<0.05),and there was no superposition effect with GLG-ZG.Conclusion GLGZG may play a neuroprotective role by inhibiting inflammatory factors and apoptosis,and inhibiting Notch signaling pathway.
10.Identification of Novel Proteins for Creutzfeldt-Jakob Disease by Integrating Genome-wide Association Data and Human Brain Proteomes
Wan-Ting ZHONG ; Yi-Tong YUAN ; Min ZHANG ; Ruo-Chen DU ; Ling-Yu ZHANG ; Chun-Fang WANG
Chinese Journal of Biochemistry and Molecular Biology 2025;41(7):1040-1047,中插1-中插26
Creutzfeldt-Jakob disease(CJD)is a rare neurodegenerative disorder characterized by abnor-malities in the prion protein(PrP),the most common form of human prion disease.Although Genome-Wide Association Studies(GWAS)have identified numerous risk genes for CJD,the mechanisms under-lying these risk loci remain poorly understood.This study aims to elucidate novel genetically prioritized candidate proteins associated with CJD in the human brain through an integrative analytical pipeline.Uti-lizing datasets from Protein Quantitative Trait Loci(pQTL)(NpQTL1=152,NpQTL2=376),expres-sion QTL(eQTL)(N=452),and the CJD GWAS(NCJD=4 110,NControls=13 569),we imple-mented a systematic analytical pipeline.This pipeline included Proteome-Wide Association Study(PWAS),Mendelian randomization(MR),Bayesian colocalization,and Transcriptome-Wide Associa-tion Study(TWAS)to identify novel genetically prioritized candidate proteins implicated in CJD patho-genesis within the brain.Through PWAS,we identified that the altered abundance of six brain proteins was significantly associated with CJD.Two genes,STX6 and PDIA4,were established as lead causal genes for CJD,supported by robust evidence(False Discovery Rate<0.05 in MR analysis;PP4/(PP3+PP4)≥0.75 in Bayesian colocalization).Specifically,elevated levels of STX6 and PDIA4 were asso-ciated with an increased risk of CJD.Additionally,TWAS demonstrated that STX6 and PDIA4 were asso-ciated with CJD at the transcriptional level.

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