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.Clinical Efficacy and Mechanism of Bupi Qingfei Prescription in Treating Stable Bronchiectasis
Zi YANG ; Guangsen LI ; Bing WANG ; Bo XU ; Jianxin WANG ; Sheng CAO ; Xinyan CHEN ; Xia SHI ; Qing MIAO
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(2):162-169
ObjectiveTo explore the clinical efficacy and mechanism of Bupi Qingfei prescription (BPQF) in treating stable bronchiectasis in the patients with syndromes of lung-spleen Qi deficiency and phlegm-heat accumulation in the lungs. MethodsA randomized, double-blind, placebo-controlled trial was conducted. Patients were randomized into BPQF and placebo control (PC) groups. On the basis of conventional Western medicine treatment, the BPQF granules and placebo were respectively administered at 10 g each time, twice a day, for a course of 24 weeks. The TCM symptom scores, Quality of Life Questionnaire for Bronchiectasis (QOL-B) scores, lung function indicators, T lymphocyte subsets, level of inflammatory factors in the sputum, level of neutrophil elastase (NE) in the sputum, and occurrence of adverse reactions were observed before and after treatment in the two groups. ResultsA total of 64 patients completed the study, encompassing 32 in the BPQF group and 32 in the PC group. After treatment, the BPQF group showed decreased TCM symptom scores (P<0.01), increased QOL-B scores (P<0.01), and declined levels of tumor necrosis factor (TNF)-α and NE (P<0.05, P<0.01). The PC group showed decreased TCM symptom (except spleen deficiency) scores (P<0.01), increased the QOL-B health cognition and respiratory symptom domain scores (P<0.05, P<0.01), and a declined TNF-α level (P<0.01). Moreover, the BPQF group had lower TCM symptom (except chest tightness) scores (P<0.05, P<0.01), higher QOL-B (except treatment burden) scores (P<0.05, P<0.01), and lower levels of interleukin-6 and TNF-α (P<0.05) than the PC group. Neither group showed serious adverse reactions during the treatment process. ConclusionBPQF can ameliorate the clinical symptoms of stable bronchiectasis patients who have lung-spleen Qi deficiency or phlegm-heat accumulation in the lungs by regulating the immune balance and inhibiting airway inflammatory responses.
3.Insights on Peripheral Blood Biomarkers for Parkinson’s Disease
Yu-Meng LI ; Jing-Kai LIU ; Zi-Xuan CHEN ; Yu-Lin DENG
Progress in Biochemistry and Biophysics 2025;52(1):72-87
Parkinson’s disease (PD) is a common neurodegenerative disorder with profound impact on patients’ quality of life and long-term health, and early detection and intervention are particularly critical. In recent years, the search for precise and reliable biomarkers has become one of the key strategies to effectively address the clinical challenges of PD. In this paper, we systematically evaluated potential biomarkers, including proteins, metabolites, epigenetic markers, and exosomes, in the peripheral blood of PD patients. Protein markers are one of the main directions of biomarker research in PD. In particular, α‑synuclein and its phosphorylated form play a key role in the pathological process of PD. It has been shown that aggregation of α-synuclein may be associated with pathologic protein deposition in PD and may be a potential marker for early diagnosis of PD. In terms of metabolites, uric acid, as a metabolite, plays an important role in oxidative stress and neuroprotection in PD. It has been found that changes in uric acid levels may be associated with the onset and progression of PD, showing its potential as an early diagnostic marker. Epigenetic markers, such as DNA methylation modifications and miRNAs, have also attracted much attention in Parkinson’s disease research. Changes in these markers may affect the expression of PD-related genes and have an important impact on the onset and progression of the disease, providing new research perspectives for the early diagnosis of PD. In addition, exosomes, as a potential biomarker carrier for PD, are able to carry a variety of biomolecules involved in intercellular communication and pathological regulation. Studies have shown that exosomes may play an important role in the pathogenesis of PD, and their detection in blood may provide a new breakthrough for early diagnosis. It has been shown that exosomes may play an important role in the pathogenesis of PD, and their detection in blood may provide new breakthroughs in early diagnosis. In summary, through in-depth evaluation of biomarkers in the peripheral blood of PD patients, this paper demonstrates the important potential of these markers in the early diagnosis of PD and in the study of pathological mechanisms. Future studies will continue to explore the clinical application value of these biomarkers to promote the early detection of PD and individualized treatment strategies.
4.Endovascular Treatment for Acute Posterior Circulation Tandem Lesions: Insights From the BASILAR and PERSIST Registries
Wei LI ; Mohamed F. DOHEIM ; Zhongming QIU ; Tan WANG ; Zhibin CHEN ; Wenjie ZI ; Qingwu YANG ; Haitao GUAN ; Hongyu QIAO ; Wenhua LIU ; Wei HU ; Xinfeng LIU ; Jinbo HUANG ; Zhongkui HAN ; Zhonglun CHEN ; Zhenqiang ZHAO ; Wen SUN ; Raul G. NOGUEIRA
Journal of Stroke 2025;27(1):75-84
Background:
and Purpose Limited evidence exists on the effectiveness of endovascular treatment (EVT) for acute posterior circulation tandem lesion (PCTL). This study aimed to explore the role of extracranial vertebral artery (VA) stenting in patients with PCTL stroke undergoing EVT.
Methods:
Individual patient data were pooled from the BASILAR (EVT for Acute Basilar Artery Occlusion Study) and PERSIST (Posterior Circulation Ischemic Stroke) registries. Patients with PCTLs who underwent EVT were included in the present cohort and divided into the stenting and nonstenting groups based on the placement of extracranial VA stents. The primary efficacy outcome was the modified Rankin Scale (mRS) scores at 90 days and 1 year. Safety outcomes included 24-hour symptomatic intracranial hemorrhage (sICH) and all-cause mortality at 90 days and 1 year post-surgery.
Results:
A combined dataset of 1,320 patients with posterior circulation artery occlusion, including 263 (19.9%) with tandem lesions, of whom 217 (median age, 65 years; 82.9% male) met the inclusion criteria for the analysis. The stenting group had 84 (38.7%) patients, while the non-stenting group had 133 (61.3%). After adjustment for the potential confounders, extracranial VA stenting was associated with favorable shifts in mRS scores at both 90 days (adjusted common odds ratio [OR], 2.30; 95% confidence interval [CI], 1.23–4.28; P<0.01) and 1 year (adjusted OR [aOR], 2.04; 95% CI [1.05–3.97]; P=0.04), along with lower rate of mortality at both 90 days (aOR, 0.45; 95% CI [0.21–0.93]; P=0.01) and 1 year (aOR, 0.36; 95% CI [0.16–0.79]; P=0.01), with no significant difference in sICH incidence (aOR, 0.35; 95% CI [0.06–1.98]; P=0.24).
Conclusion
Extracranial VA stenting during EVT may improve functional outcomes and reduce mortality in patients with PCTL strokes.
5.Effects of electroacupuncture on the expression of metabolic enzymes and autophagy genes in gastrocnemius muscle tissues of exercising rats
Rongfa ZHENG ; Weibin MO ; Peng HUANG ; Junji CHEN ; Ting LIANG ; Fangyu ZI ; Guofeng LI
Chinese Journal of Tissue Engineering Research 2025;29(6):1127-1136
BACKGROUND:Acute exercise tends to cause skeletal muscle tissue damage and lipid metabolism disorders in vivo,but the mechanism by which acute exercise combined with electroacupuncture modulates metabolic and autophagic pathways in vivo is unclear. OBJECTIVE:To observe the changes in metabolic enzymes and autophagy levels in skeletal muscle of rats subjected to acute exercise by electroacupuncture at the acupoints of"Zusanli"and"Huantiao." METHODS:Fifty male Sprague-Dawley rats were randomly divided into three groups:quiet control group(n=10),model group(n=20),and reverse electroacupuncture group(n=20).The latter two groups were set up with two time points,i.e.immediate and 3 hours after exercise groups(n=10 per time point).The model group and the reverse electroacupuncture group underwent acute exercise training after adaptive treadmill training.The rats in the reverse electroacupuncture group underwent electroacupuncture treatment(parameters:electroacupuncture on both sides of the rats at the acupoints of"Zusanli"and"Huantiao,"continuous wave,frequency of 2 Hz,intensity of 2 mA,leaving the needle in the body for 30 minutes,once a day for 7 consecutive days)before treadmill training.Bilateral gastrocnemius muscle tissues were taken under anesthesia immediately after exercise and 3 hours after exercise,and hematoxylin-eosin staining was used to observe the histopathological changes of rat skeletal muscle.ELISA kit was used to detect the activities of hepatic lipase,fatty acid synthase,hormone-sensitive lipase,and carnitine palmitoyltransferase 1 in rat skeletal muscle tissues.Immunohistochemistry and western blot were used to detect the changes in the expression of autophagy genes. RESULTS AND CONCLUSION:After hematoxylin-eosin staining,the arrangement of gastrocnemius muscle fibers in the model group was disturbed,swollen and ruptured immediately after exercise and 3 hours after exercise.In the reverse electroacupuncture group,gastrocnemius muscle fibers were tightly arranged and the number of swollen and ruptured cells was greatly reduced immediately after exercise and 3 hours after exercise,and there was no significant difference when compared with the quiet control group.Compared with the quiet control group,the activities of hepatic lipase and fatty acid synthase were lower while the activities of lipoprotein lipase,hormone-sensitive lipase,and carnitine palmitoyltransferase 1 were higher in the model group and the reverse electroacupuncture group 3 hours after exercise(P<0.05 or P<0.01).Compared with the model group,the activities of lipoprotein lipase and carnitine palmitoyltransferase 1 were higher in the reverse electroacupuncture group immediately after exercise(P<0.05),while the activity of lipoprotein lipase was higher and the activity of hormone-sensitive lipase was lower in the reverse electroacupuncture group 3 hours after exercise(P<0.01).Immunohistochemical results showed that compared with the quiet control group,the expression of P62,autophagy-related gene 5 and autophagy-related gene 7 was higher in the model group immediately and 3 hours after exercise,as well as in the reverse electroacupuncture group immediately after exercise(P<0.05 or P<0.01);compared with the model group,the expression of P62 and autophagy-related gene 7 was lower in the reverse electroacupuncture group immediately and 3 hours after exercise(P<0.05).Western blot results showed that the protein expression of P62 and autophagy-related gene 7 in the reverse electroacupuncture group was lower than that in the model group immediately after exercise(P<0.05);the protein expression of Parkin in the model group was higher than that in the quiet control group immediately and 3 hours after exercise(P<0.05);and the protein expression of Parkin in the reverse electroacupuncture group was lower than that in the model group immediately and 3 hours after exercise(P<0.05).To conclude,acute exercise induces disorders,swelling and rupture of gastrocnemius muscle fibers in rats and electroacupuncture on both sides of the acupoints of"Zusanli"and"Huantiao"can improve the level of lipid metabolism and regulate autophagy cells in rat skeletal muscle,preventing the disorders of lipid metabolism and damage of gastrocnemius muscle tissues caused by acute exercise.The mechanism may be closely related to the regulation of autophagy-related factor P62,autophagy-related gene 5,autophagy-related gene 7,and Parkin protein expression to promote the occurrence of autophagy or regulate the autophagy pathway in rat skeletal muscle cells.
6.Targeted screening and profiling of massive components of colistimethate sodium by two-dimensional-liquid chromatography-mass spectrometry based on self-constructed compound database
Xuan LI ; Minwen HUANG ; Yue-Mei ZHAO ; Wenxin LIU ; Nan HU ; Jie ZHOU ; Zi-Yi WANG ; Sheng TANG ; Jian-Bin PAN ; Kee-Lee HIAN ; Yao-Zuo YUAN ; Taijun HANG ; Hai-Wei SHI ; Hongyuan CHEN
Journal of Pharmaceutical Analysis 2025;15(2):401-410
In-depth study of the components of polymyxins is the key to controlling the quality of this class of antibiotics.Similarities and variations of components present significant analytical challenges.A two-dimensional(2D)liquid chromatography-mass spectrometry(LC-MS)method was established for screening and comprehensive profiling of compositions of the antibiotic colistimethate sodium(CMS).A high concentration of phosphate buffer mobile phase was used in the first-dimensional LC system to get the components well separated.For efficient and high-accuracy screening of CMS,a targeted method based on a self-constructed high resolution(HR)mass spectrum database of CMS components was established.The database was built based on the commercial MassHunter Personal Compound Database and Library(PCDL)software and its accuracy of the compound matching result was verified with six known components before being applied to genuine sample screening.On this basis,the unknown peaks in the CMS chromatograms were deduced and assigned.The molecular formula,group composition,and origins of a total of 99 compounds,of which the combined area percentage accounted for more than 95%of CMS components,were deduced by this 2D-LC-MS method combined with the MassHunter PCDL.This profiling method was highly efficient and could distinguish hundreds of components within 3 h,providing reliable results for quality control of this kind of complex drugs.
7.Clinical effects of Jiawei Yanghe Decoction combined with Budesonide and Formoterol Fumarate Powder for Inhalation on patients with mild to moderate bronchial asthma in chronic and persistent period
Yu WANG ; Hui-yong ZHANG ; Lin-jin CHEN ; Zheng-yi ZHANG ; Cui LI ; Jie CUI ; Ben SU ; Ping BAI ; Zi-feng MA ; Zhen-hui LU
Chinese Traditional Patent Medicine 2025;47(1):81-86
AIM To explore the clinical effects of Jiawei Yanghe Decoction combined with Budesonide and Formoterol Fumarate Powder for Inhalation on patients with mild to moderate bronchial asthma in chronic and persistent period.METHODS One hundred and eighteen patients were randomly assigned into control group(59 cases)for 4-week administration of Budesonide and Formoterol Fumarate Powder for Inhalation,and observation group(59 cases)for 4-week administration of both Jiawei Yanghe Decoction and Budesonide and Formoterol Fumarate Powder for Inhalation.The changes in clinical effects,ACT score,bronchial asthma control rate,pulmonary function indices(FEV1,PEF,FEV1%,PEF%),inflammatory indices(EOS,EOS%,FeNO),TCM syndrome score and incidence of adverse reactions were detected.RESULTS The observation group demonstrated higher total effective rate than the control group(P<0.05).After the treatment,the two groups displayed increased bronchial asthma control rate,ACT score,PEF(P<0.05),and decreased TCM syndrome score(P<0.05),especially for the observation group(P<0.05);the observation group exhibited increased FEV1,FEV1%,PEF%(P<0.05),among which FEV1,PEF%were higher than those in the control group(P<0.05);the observation group showed decreased inflammatory indices(P<0.05),among which FeNO was lower than that in the control group(P<0.05).No significant difference in incidence of adverse reactions was found between the two groups(P>0.05).CONCLUSION For the patients with mild to moderate bronchial asthma in chronic and persistent period,Jiawei Yanghe Decoction combined with Budesonide and Formoterol Fumarate Powder for Inhalation can safely and effectively alleviate clinical symptoms,improve pulmonary functions,airway inflammatory reactions,and enhance bronchial asthma control rate.
8.Effect of simultaneous integrated boost IMRT on quality of life in patients with advanced nasopharyngeal carcinoma
Bin LIU ; Zi CHEN ; Zhihui HU ; Yan LI ; Kun CHEN
Chinese Journal of Medical Physics 2025;42(5):577-580
Objective To explore and analyze the clinical efficacy of simultaneous integrated boost intensity-modulated radiotherapy(IMRT)and its effect on quality of life in advanced nasopharyngeal carcinoma(NPC)patients.Methods A retrospective analysis was conducted on 62 patients with advanced NPC.Patients were divided into trial group(n=31,simultaneous integrated boost IMRT+chemotherapy)and control group(n=31,conventional IMRT+chemotherapy)according to different treatment regimens.The two groups were compared for objective response rate,disease control rate,recurrence and metastasis rate,long-term survival rate,quality of life score,and incidence of adverse reactions.Results Compared with control group,trial group resulted in higher objective response rate,disease control rate and long-term survival rate,while lower recurrence and metastasis rate,post-therapy quality of life score and incidence of adverse reactions(all P<0.05).Conclusion Patients with advanced NPC show remarkable response to simultaneous integrated boost IMRT which can reduce recurrence and metastasis rate,prolong survival cycle,improve quality of life,and lower incidence of adverse reactions.
9.Selection of exosomal microRNA biomarkers for brucellosis diagnosis and construction of a potential miRNA-mRNA regulation network
Jin ZHAO ; Zhi-qiang CHEN ; Bing-Li WANG ; Shu-ling LI ; Xiao-yu ZHU ; Jin-tong JIA ; Ye-zi LIU ; Zhi-wei LI
Chinese Journal of Zoonoses 2025;41(3):269-277
This study was aimed at exploring novel auxiliary diagnostic biomarkers for brucellosis and their potential miR-NA-mRNA regulatory networks.High-throughput sequencing was used to compare miRNA expression differences in serum ex-osomes between patients with brucellosis and healthy controls.Subsequently,RT-qPCR was used to validate the expression of significantly upregulated exosomal miRNAs.The diagnostic value of these miRNAs was assessed with ROC curves,and bioin-formatics analyses were performed to investigate the potential roles of the miRNAs in brucellosis infection.The ROC curve a-nalysis indicated that the area under the curve for exosomal hsa-miR-11400(P<0.05),hsa-miR-199a-5p(P<0.05),and hsa-miR-148a-5p(P<0.05)was 0.79,0.81,and 0.74,respectively.A total of 465 differentially expressed miRNAs and their tar-get genes were predicted,including 25 immune-related target genes,most of which were closely associated with cancer-related proteoglycans,NF-kappa B signaling pathways,and IL-17 signaling pathways.The constructed differentially expressed gene network indicated that the immune genes PLXNA2,IL17RA,PRKCA,CD22,ACVR1B,and CBL might be regulated by hsa-miR-199a-5p and hsa-miR-148a-5p.These findings suggest that exosomal miRNAs might serve as auxiliary diagnostic indicators for brucellosis.Our exosomal miRNA-mRNA regulatory network provides new insights into the pathogenesis and treatment of brucellosis.
10.Determination of Lipid Components in Fingerprints by Gas Chromatography-Mass Spectrometry and Gender Recognition of Fingerprint Donors by Machine Learning
Zi-Chen YI ; Wen-Ji ZHANG ; Zi-Yong ZHU ; Wei YI ; Jia-Si JIANG ; Zi-Hua LI
Chinese Journal of Analytical Chemistry 2025;53(8):1290-1299,中插19-中插22
Gender recognition based on the analysis of fingerprint residue can assist investigators in narrowing down the scope of investigation and play an important role in the field of criminal investigation.This study established a quantitative analysis method for lipid substances in fingerprints based on gas chromatography-mass spectrometry(GC-MS).Fatty acids in fingerprints were methylated using sulfuric acid methanol derivatization reagent(7%,V/V),the extraction reagent was dichloromethane-methanol(1∶1,V/V)solution,the reaction temperature was 70℃and the heating time was 45 min.Quantitative analysis of the relative content of 23 kinds of fatty acids and squalene in fingerprints residue by different genders was conducted,and orthogonal partial least squares-discriminant analysis(OPLS-DA)was used to reduce the dimensionality of the quantitative results.A total of 13 kinds of components in the fingerprints were selected to maximize the difference in relative content between male and female fingerprints.Three machine learning models,including binary logistic regression(BLR),support vector machine(SVM)and random forest(RF),were further used as feature variables to classify the gender of fingerprints.The classification performance of each model was compared through five indicators,and it was found that the most suitable model for binary classification of fingerprint gender was SVM model.The results showed that the SVM fingerprint residual gender binary classification model established based on the relative content data of 13 kinds of lipid substances in fingerprints achieved a classification accuracy of 90%and an area under the receiver operating characteristic curve(AUC)value of 0.98.This study provided a new research method for detecting lipid components in fingerprints and a methodological basis for gender recognition of fingerprints.

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