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.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.
3.Mechanisms and intervention strategies of aging based on epigenetics
Li-yuan ZHANG ; Hao-nan SHI ; Wen-feng ZHANG ; Ming-qian ZHANG ; Zi-yang ZHAO ; Zhen-zhen CHENG ; Ti ZHANG ; Zhen-teng YAN ; Jian-ning SUN ; Shi-fen DONG
Chinese Pharmacological Bulletin 2025;41(12):2230-2235
Aging is comprehensively influenced by multiple fac-tors such as internal genes,cellular metabolism,external envi-ronment,and lifestyle habits.Among them,epigenetic regula-tion plays a core role.Epigenetic modifications,including DNA methylation,histone modification,heterochromatin remodeling,and non-coding RNA regulation,act in concert with the three-di-mensional genome architecture to precisely regulate gene expres-sion.This review elaborates on the factors influencing epigenetic regulation,as well as the mechanisms of how epigenetics affects the occurrence of organismal aging and the corresponding inter-vention strategies,providing relevant insights for uncovering the mechanisms of aging and preventing/treating aging-related disea-ses.
4.EEG phase prediction method based on long short-term memory network
Zi-yan PANG ; Xin-yu ZHAO ; Wen-shu MAI ; Yue-zhuo ZHAO ; Zhi-peng LIU ; Tao YIN ; Jing-na JIN
Chinese Medical Equipment Journal 2025;46(3):1-8
Objective To propose a brain electrical phase prediction method based on long short-term memory network(LSTM)to improve the accuracy and robustness of phase synchronization prediction in transcranial magnetic stimulation(TMS).Methods First,an LSTM consisting of an input layer,an LSTM layer,an ReLU activation layer,a fully connected layer and a regression layer was constructed to capture the EEG signal features through the synergistic action of input gates,forgetting gates and output gates.Second,eye-open resting-state EEG data from 30 healthy subjects were trained using the LSTM to obtain a predictive model for EEG signal and EEG phase prediction.Finally,the LSTM method and the traditional autoregressive(AR)method were compared in terms of the phase prediction errors at the overall and individual levels and the prediction performance for peaks and troughs.A regression model was used to explore the relationships between instantaneous EEG amplitude,signal-to-noise ratio and phase prediction error with the LSTM method.Results The LSTM method achieved a total phase prediction error of 0.04°±5.69°,which was lower than that of the traditional AR method(-3.36°±51.13°).For each subject,the LSTM method demonstrated superior phase prediction accuracy compared to the traditional AR method(P<0.001).The accuracy for predicting peaks(troughs)by the LSTM method(about 89%)was higher than that by the traditional AR method(about 10%).Unlike the traditional AR method,the LSTM method didnot result in linear relationships between instantaneous EEG amplitude,signal-to-noise ratio and phase prediction error,with Pvalues being 0.58 and 0.18,respectively.Conclusion The LSTM-based brain electrical phase prediction method shows high accuracy and robustness when used for EEG phase-synchronized TMS.[Chinese Medical Equipment Journal,2025,46(3):1-8]
5.EEG phase prediction method based on long short-term memory network
Zi-yan PANG ; Xin-yu ZHAO ; Wen-shu MAI ; Yue-zhuo ZHAO ; Zhi-peng LIU ; Tao YIN ; Jing-na JIN
Chinese Medical Equipment Journal 2025;46(3):1-8
Objective To propose a brain electrical phase prediction method based on long short-term memory network(LSTM)to improve the accuracy and robustness of phase synchronization prediction in transcranial magnetic stimulation(TMS).Methods First,an LSTM consisting of an input layer,an LSTM layer,an ReLU activation layer,a fully connected layer and a regression layer was constructed to capture the EEG signal features through the synergistic action of input gates,forgetting gates and output gates.Second,eye-open resting-state EEG data from 30 healthy subjects were trained using the LSTM to obtain a predictive model for EEG signal and EEG phase prediction.Finally,the LSTM method and the traditional autoregressive(AR)method were compared in terms of the phase prediction errors at the overall and individual levels and the prediction performance for peaks and troughs.A regression model was used to explore the relationships between instantaneous EEG amplitude,signal-to-noise ratio and phase prediction error with the LSTM method.Results The LSTM method achieved a total phase prediction error of 0.04°±5.69°,which was lower than that of the traditional AR method(-3.36°±51.13°).For each subject,the LSTM method demonstrated superior phase prediction accuracy compared to the traditional AR method(P<0.001).The accuracy for predicting peaks(troughs)by the LSTM method(about 89%)was higher than that by the traditional AR method(about 10%).Unlike the traditional AR method,the LSTM method didnot result in linear relationships between instantaneous EEG amplitude,signal-to-noise ratio and phase prediction error,with Pvalues being 0.58 and 0.18,respectively.Conclusion The LSTM-based brain electrical phase prediction method shows high accuracy and robustness when used for EEG phase-synchronized TMS.[Chinese Medical Equipment Journal,2025,46(3):1-8]
6.Mechanisms and intervention strategies of aging based on epigenetics
Li-yuan ZHANG ; Hao-nan SHI ; Wen-feng ZHANG ; Ming-qian ZHANG ; Zi-yang ZHAO ; Zhen-zhen CHENG ; Ti ZHANG ; Zhen-teng YAN ; Jian-ning SUN ; Shi-fen DONG
Chinese Pharmacological Bulletin 2025;41(12):2230-2235
Aging is comprehensively influenced by multiple fac-tors such as internal genes,cellular metabolism,external envi-ronment,and lifestyle habits.Among them,epigenetic regula-tion plays a core role.Epigenetic modifications,including DNA methylation,histone modification,heterochromatin remodeling,and non-coding RNA regulation,act in concert with the three-di-mensional genome architecture to precisely regulate gene expres-sion.This review elaborates on the factors influencing epigenetic regulation,as well as the mechanisms of how epigenetics affects the occurrence of organismal aging and the corresponding inter-vention strategies,providing relevant insights for uncovering the mechanisms of aging and preventing/treating aging-related disea-ses.
7.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.
8.Analysis of risk factors, pathogenic bacteria characteristics, and drug resistance of postoperative surgical site infection in adults with limb fractures.
Yan-Jun WANG ; Zi-Hou ZHAO ; Shuai-Kun LU ; Guo-Liang WANG ; Shan-Jin MA ; Lin-Hu WANG ; Hao GAO ; Jun REN ; Zhong-Wei AN ; Cong-Xiao FU ; Yong ZHANG ; Wen LUO ; Yun-Fei ZHANG
Chinese Journal of Traumatology 2025;28(4):241-251
PURPOSE:
We carried out the study aiming to explore and analyze the risk factors, the distribution of pathogenic bacteria, and their antibiotic-resistance characteristics influencing the occurrence of surgical site infection (SSI), to provide valuable assistance for reducing the incidence of SSI after traumatic fracture surgery.
METHODS:
A retrospective case-control study enrolling 3978 participants from January 2015 to December 2019 receiving surgical treatment for traumatic fractures was conducted at Tangdu Hospital of Air Force Medical University. Baseline data, demographic characteristics, lifestyles, variables related to surgical treatment, and pathogen culture were harvested and analyzed. Univariate analyses and multivariate logistic regression analyses were used to reveal the independent risk factors of SSI. A bacterial distribution histogram and drug-sensitive heat map were drawn to describe the pathogenic characteristics.
RESULTS:
Included 3978 patients 138 of them developed SSI with an incidence rate of 3.47% postoperatively. By logistic regression analysis, we found that variables such as gender (males) (odds ratio (OR) = 2.012, 95% confidence interval (CI): 1.235 - 3.278, p = 0.005), diabetes mellitus (OR = 5.848, 95% CI: 3.513 - 9.736, p < 0.001), hypoproteinemia (OR = 3.400, 95% CI: 1.280 - 9.031, p = 0.014), underlying disease (OR = 5.398, 95% CI: 2.343 - 12.438, p < 0.001), hormonotherapy (OR = 11.718, 95% CI: 6.269 - 21.903, p < 0.001), open fracture (OR = 29.377, 95% CI: 9.944 - 86.784, p < 0.001), and intraoperative transfusion (OR = 2.664, 95% CI: 1.572 - 4.515, p < 0.001) were independent risk factors for SSI, while, aged over 59 years (OR = 0.132, 95% CI: 0.059 - 0.296, p < 0.001), prophylactic antibiotics use (OR = 0.082, 95% CI: 0.042 - 0.164, p < 0.001) and vacuum sealing drainage use (OR = 0.036, 95% CI: 0.010 - 0.129, p < 0.001) were protective factors. Pathogens results showed that 301 strains of 38 species of bacteria were harvested, among which 178 (59.1%) strains were Gram-positive bacteria, and 123 (40.9%) strains were Gram-negative bacteria. Staphylococcus aureus (108, 60.7%) and Enterobacter cloacae (38, 30.9%) accounted for the largest proportion. The susceptibility of Gram-positive bacteria to Vancomycin and Linezolid was almost 100%. The susceptibility of Gram-negative bacteria to Imipenem, Amikacin, and Meropenem exceeded 73%.
CONCLUSION
Orthopedic surgeons need to develop appropriate surgical plans based on the risk factors and protective factors associated with postoperative SSI to reduce its occurrence. Meanwhile, it is recommended to strengthen blood glucose control in the early stage of admission and for surgeons to be cautious and scientific when choosing antibiotic therapy in clinical practice.
Humans
;
Surgical Wound Infection/epidemiology*
;
Male
;
Female
;
Risk Factors
;
Retrospective Studies
;
Middle Aged
;
Adult
;
Case-Control Studies
;
Fractures, Bone/surgery*
;
Aged
;
Drug Resistance, Bacterial
;
Logistic Models
;
Anti-Bacterial Agents/therapeutic use*
;
Incidence
;
Bacteria/drug effects*
9.Progress in Animal and Clinical Studies on the Impact of Bisphosphonates on Implant Stability.
Ling-Lu JIA ; Zi-Kai GONG ; Wen-Xi ZHAO ; Yong WEN
Acta Academiae Medicinae Sinicae 2025;47(4):628-633
Bisphosphonates(BP),a class of commonly used medications for treating osteoporosis and bone malignancies,significantly affect bone metabolism.When dental implants are placed in patients receiving BP,the potential impacts of BP on the formation and long-term maintenance of implant osseointegration cannot be ignored.In addition,the influence of dental implants on the occurrence of BP-related osteonecrosis of the jaw is garnering attention.This article explores the influences of BP on the stability of dental implants based on a review of previous animal and clinical studies,discusses the impact of dental implants on the occurrence of BP-related osteonecrosis of the jaw,and proposes suggestions for the dental implant treatment of patients taking BP in clinical practice.This review is expected to provide a theoretical basis for the related research and clinical treatment.
Humans
;
Dental Implants
;
Animals
;
Diphosphonates/pharmacology*
;
Osseointegration/drug effects*
;
Bisphosphonate-Associated Osteonecrosis of the Jaw
10.Qingda Granule Attenuates Hypertension-Induced Cardiac Damage via Regulating Renin-Angiotensin System Pathway.
Lin-Zi LONG ; Ling TAN ; Feng-Qin XU ; Wen-Wen YANG ; Hong-Zheng LI ; Jian-Gang LIU ; Ke WANG ; Zhi-Ru ZHAO ; Yue-Qi WANG ; Chao-Ju WANG ; Yi-Chao WEN ; Ming-Yan HUANG ; Hua QU ; Chang-Geng FU ; Ke-Ji CHEN
Chinese journal of integrative medicine 2025;31(5):402-411
OBJECTIVE:
To assess the efficacy of Qingda Granule (QDG) in ameliorating hypertension-induced cardiac damage and investigate the underlying mechanisms involved.
METHODS:
Twenty spontaneously hypertensive rats (SHRs) were used to develope a hypertension-induced cardiac damage model. Another 10 Wistar Kyoto (WKY) rats were used as normotension group. Rats were administrated intragastrically QDG [0.9 g/(kg•d)] or an equivalent volume of pure water for 8 weeks. Blood pressure, histopathological changes, cardiac function, levels of oxidative stress and inflammatory response markers were measured. Furthermore, to gain insights into the potential mechanisms underlying the protective effects of QDG against hypertension-induced cardiac injury, a network pharmacology study was conducted. Predicted results were validated by Western blot, radioimmunoassay immunohistochemistry and quantitative polymerase chain reaction, respectively.
RESULTS:
The administration of QDG resulted in a significant decrease in blood pressure levels in SHRs (P<0.01). Histological examinations, including hematoxylin-eosin staining and Masson trichrome staining revealed that QDG effectively attenuated hypertension-induced cardiac damage. Furthermore, echocardiography demonstrated that QDG improved hypertension-associated cardiac dysfunction. Enzyme-linked immunosorbent assay and colorimetric method indicated that QDG significantly reduced oxidative stress and inflammatory response levels in both myocardial tissue and serum (P<0.01).
CONCLUSIONS
Both network pharmacology and experimental investigations confirmed that QDG exerted its beneficial effects in decreasing hypertension-induced cardiac damage by regulating the angiotensin converting enzyme (ACE)/angiotensin II (Ang II)/Ang II receptor type 1 axis and ACE/Ang II/Ang II receptor type 2 axis.
Animals
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Drugs, Chinese Herbal/therapeutic use*
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Hypertension/pathology*
;
Renin-Angiotensin System/drug effects*
;
Rats, Inbred SHR
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Oxidative Stress/drug effects*
;
Male
;
Rats, Inbred WKY
;
Blood Pressure/drug effects*
;
Myocardium/pathology*
;
Rats
;
Inflammation/pathology*

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