1.The Role of Neuroinflammation and Network Anomalies in Drug-Resistant Epilepsy.
Jianwei SHI ; Jing XIE ; Zesheng LI ; Xiaosong HE ; Penghu WEI ; Josemir W SANDER ; Guoguang ZHAO
Neuroscience Bulletin 2025;41(5):881-905
Epilepsy affects over 50 million people worldwide. Drug-resistant epilepsy (DRE) accounts for up to a third of these cases, and neuro-inflammation is thought to play a role in such cases. Despite being a long-debated issue in the field of DRE, the mechanisms underlying neuroinflammation have yet to be fully elucidated. The pro-inflammatory microenvironment within the brain tissue of people with DRE has been probed using single-cell multimodal transcriptomics. Evidence suggests that inflammatory cells and pro-inflammatory cytokines in the nervous system can lead to extensive biochemical changes, such as connexin hemichannel excitability and disruption of neurotransmitter homeostasis. The presence of inflammation may give rise to neuronal network abnormalities that suppress endogenous antiepileptic systems. We focus on the role of neuroinflammation and brain network anomalies in DRE from multiple perspectives to identify critical points for clinical application. We hope to provide an insightful overview to advance the quest for better DRE treatments.
Humans
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Drug Resistant Epilepsy/metabolism*
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Neuroinflammatory Diseases/immunology*
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Animals
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Brain/pathology*
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Nerve Net/pathology*
2.Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.
Heng WANG ; Ang WU ; Meng-Chen YANG ; Di ZHOU ; Xiyang CHEN ; Zhifei SHI ; Yiqun ZHANG ; Yu-Xin LIU ; Kai CHEN ; Xiaosong WANG ; Xiao-Fang CHENG ; Baodan HE ; Yutao FU ; Lan KANG ; Yujun HOU ; Kun CHEN ; Shan BIAN ; Juan TANG ; Jianhuang XUE ; Chenfei WANG ; Xiaoyu LIU ; Jiejun SHI ; Shaorong GAO ; Jia-Min ZHANG
Protein & Cell 2025;16(11):932-952
Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin regions, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at the single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences on TF binding. Notably, cFOOT-seq, combined with FootTrack analysis, enables de novo prediction of TF binding sites and tracking of TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.
Transcription Factors/genetics*
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Humans
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Chromatin/genetics*
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Animals
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Binding Sites
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Mice
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DNA Footprinting/methods*
3.Heart failure prediction model based on machine learning algorithms
Chuanli HU ; Xiaosong HE ; Jiang ZHAO ; Hua LI
Basic & Clinical Medicine 2024;44(6):845-852
Objective To construct a model of heart failure risk prediction based on four machine learning algo-rithms in order to support early diagnosis and intervention.Methods After reviewing the heart failure dataset pub-lished on the Kaggle community,feature selection was used to select relevant factors related to heart failure as pre-dictive indicators.Four machine learning algorithms,namely logistic regression,support vector machine,random forest,and XGBoost were selected to establish predictive models.Compared and analyzed its accuracy,precision,recall,F1 score and area under the ROC curve(AUC)to verify the performance of the model.Results The study analyzed 11 features of 918 patients with heart failure and selected 10 feature factors for modeling.After optimizing the hyper-parameters through grid search,the XGBoost model performed the best,with accuracy,precision,recall,and f1_score and AUC values were 87.5%,90.38%,89.71%,90.04%and 0.93,respectively.In addition,data analysis showed that exercise ST slope,chest pain type,and exercise induced angina were main influencing factors for heart failure.Conclusions The XG Boost model has the best predictive tool for heart failure,and machine learning algorithms may support early prevention,early diagnosis as well as control of heart failure.
4.Application and economic effects of digital three-dimensional reconstruction in hip hemiarthroplasty for intertrochanteric femoral fractures in the elderly
Peng LI ; Xiaosong HAN ; Bingyan XIANG ; Yingyi HE ; Kun HUANG ; Li LIU ; Hongjian LUO ; Shiqiang RUAN
Chinese Journal of Tissue Engineering Research 2024;28(18):2814-2818
BACKGROUND:Digital three-dimensional reconstruction technology is gradually applied to orthopedic diseases with the advantages of visualization,accuracy and non-invasiveness,but there is less evidence-based support for its use in artificial hip hemiarthroplasty for intertrochanteric fractures of the femur in the elderly. OBJECTIVE:To investigate the application value and economic effects of digital three-dimensional reconstruction techniques in artificial hip hemiarthroplasty of intertrochanteric fractures of the femur in the elderly. METHODS:One hundred and thirty elderly patients with intertrochanteric femur fractures admitted to Zunyi First People's Hospital from January 2019 to December 2022 were selected and randomly divided into a control group(n=65)and an observation group(n=65).Artificial hip hemiarthroplasty was performed in both groups.The control group adopted the film template measurement method for manual preoperative planning while the observation group adopted a digital three-dimensional reconstruction technique.Preoperative planning and intraoperative actual application of prosthesis compliance rate,fibrinogen,D-dimer,bilateral femoral eccentric distance difference,bilateral lower limb length difference,Harris hip function score,visual analog scale score,excellent and good rate of hip function,complications,and hospitalization cost were observed in both groups. RESULTS AND CONCLUSION:(1)The proportion of acetabular side and femoral side prosthesis in grade 0(fully compliant)was higher in the observation group than that in the control group(P<0.05).(2)Fibrinogen and D-dimer levels in the observation group were lower than those in the control group 3 days after surgery(P<0.05).(3)The difference in bilateral femoral eccentric distance and the difference in bilateral lower limb length in the observation group were smaller than those in the control group immediately after surgery(P<0.05).The differences in Harris and visual analog scale scores were not significantly different between the two groups preoperatively,6 and 12 months postoperatively(P>0.05).There was no significant difference in excellent and good rate of hip function between the two groups 12 months postoperatively(P>0.05).(4)There was no significant difference in the complication rate between the two groups(P>0.05).The hospitalization cost of the observation group was higher than that of the control group(P<0.05).(5)It is indicated that digital three-dimensional reconstruction technology applied in artificial hip hemiarthroplasty of intertrochanteric femoral fracture in the elderly can not only accurately determine the prosthesis type before surgery,but also accurately reconstruct the bilateral lower limbs offline,but its hospitalization cost is high.
5.Exploration of ethical issues in neuroimaging data sharing
Chinese Medical Ethics 2024;37(6):669-676
In recent years,countries around the world have invested a lot of resources in neuroimaging research on brain function and diseases.The abundant and more easily accessible neuroimaging data will have a profound impact on the research of cognitive neuroscience and psychiatry,thereby assisting the development of the diagnosis and treatment of brain diseases.At present,neuroimaging data sharing is gradually becoming a trend,but it is also worth considering of some unique ethical issues that come with it.Therefore,from the four shared entities of the public,researchers,users,and data centers,this paper sorted out the ethical issues in neuroimaging data sharing,and deeply analyzed the reasons for these issues.Based on the responsibility ethics and combined with the guidance of the Belmont principles,governance responses were proposed,including strengthening the construction of neuroethics committees,improving informed consent models,building data sharing infrastructure,establishing data privacy protection mechanisms,and introducing regulatory protections,to provide a certain reference for promoting the neuroimaging data sharing and maximizing the contribution of participants.
6.Chinese expert consensus on emergency surgery for severe trauma and infection prevention during corona virus disease 2019 epidemic (version 2023)
Yang LI ; Yuchang WANG ; Haiwen PENG ; Xijie DONG ; Guodong LIU ; Wei WANG ; Hong YAN ; Fan YANG ; Ding LIU ; Huidan JING ; Yu XIE ; Manli TANG ; Xian CHEN ; Wei GAO ; Qingshan GUO ; Zhaohui TANG ; Hao TANG ; Bingling HE ; Qingxiang MAO ; Zhen WANG ; Xiangjun BAI ; Daqing CHEN ; Haiming CHEN ; Min DAO ; Dingyuan DU ; Haoyu FENG ; Ke FENG ; Xiang GAO ; Wubing HE ; Peiyang HU ; Xi HU ; Gang HUANG ; Guangbin HUANG ; Wei JIANG ; Hongxu JIN ; Laifa KONG ; He LI ; Lianxin LI ; Xiangmin LI ; Xinzhi LI ; Yifei LI ; Zilong LI ; Huimin LIU ; Changjian LIU ; Xiaogang MA ; Chunqiu PAN ; Xiaohua PAN ; Lei PENG ; Jifu QU ; Qiangui REN ; Xiguang SANG ; Biao SHAO ; Yin SHEN ; Mingwei SUN ; Fang WANG ; Juan WANG ; Jun WANG ; Wenlou WANG ; Zhihua WANG ; Xu WU ; Renju XIAO ; Yang XIE ; Feng XU ; Xinwen YANG ; Yuetao YANG ; Yongkun YAO ; Changlin YIN ; Yigang YU ; Ke ZHANG ; Xingwen ZHANG ; Guixi ZHANG ; Gang ZHAO ; Xiaogang ZHAO ; Xiaosong ZHU ; Yan′an ZHU ; Changju ZHU ; Zhanfei LI ; Lianyang ZHANG
Chinese Journal of Trauma 2023;39(2):97-106
During coronavirus disease 2019 epidemic, the treatment of severe trauma has been impacted. The Consensus on emergency surgery and infection prevention and control for severe trauma patients with 2019 novel corona virus pneumonia was published online on February 12, 2020, providing a strong guidance for the emergency treatment of severe trauma and the self-protection of medical staffs in the early stage of the epidemic. With the Joint Prevention and Control Mechanism of the State Council renaming "novel coronavirus pneumonia" to "novel coronavirus infection" and the infection being managed with measures against class B infectious diseases since January 8, 2023, the consensus published in 2020 is no longer applicable to the emergency treatment of severe trauma in the new stage of epidemic prevention and control. In this context, led by the Chinese Traumatology Association, Chinese Trauma Surgeon Association, Trauma Medicine Branch of Chinese International Exchange and Promotive Association for Medical and Health Care, and Editorial Board of Chinese Journal of Traumatology, the Chinese expert consensus on emergency surgery for severe trauma and infection prevention during coronavirus disease 2019 epidemic ( version 2023) is formulated to ensure the effectiveness and safety in the treatment of severe trauma in the new stage. Based on the policy of the Joint Prevention and Control Mechanism of the State Council and by using evidence-based medical evidence as well as Delphi expert consultation and voting, 16 recommendations are put forward from the four aspects of the related definitions, infection prevention, preoperative assessment and preparation, emergency operation and postoperative management, hoping to provide a reference for severe trauma care in the new stage of the epidemic prevention and control.
7.Prognostic value of the 21-gene recurrence score in ER-positive, HER2-negative, node-positive breast cancer was similar in node-negative diseases: a single-center study of 800 patients.
Jiayi WU ; Weiqi GAO ; Xiaosong CHEN ; Chunxiao FEI ; Lin LIN ; Weiguo CHEN ; Ou HUANG ; Siji ZHU ; Jianrong HE ; Yafen LI ; Li ZHU ; Kunwei SHEN
Frontiers of Medicine 2021;15(4):621-628
Multi-gene assays have emerged as crucial tools for risk stratification in early-stage breast cancer. This study aimed to evaluate the prognostic significance of the 21-gene recurrence score (RS) in Chinese patients with pN0-1, estrogen receptor-positive (ER
Biomarkers, Tumor/genetics*
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Breast Neoplasms/pathology*
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Female
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Humans
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Neoplasm Recurrence, Local/pathology*
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Neoplasm Staging
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Prognosis
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Receptor, ErbB-2/genetics*
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Receptors, Estrogen
8.COVID-ONE-hi:The One-stop Database for COVID-19-specific Humoral Immunity and Clinical Parameters
Xu ZHAOWEI ; Li YANG ; Lei QING ; Huang LIKUN ; Lai DAN-YUN ; Guo SHU-JUAN ; Jiang HE-WEI ; Hou HONGYAN ; Zheng YUN-XIAO ; Wang XUE-NING ; Wu JIAOXIANG ; Ma MING-LIANG ; Zhang BO ; Chen HONG ; Yu CAIZHENG ; Xue JUN-BIAO ; Zhang HAI-NAN ; Qi HUAN ; Yu SIQI ; Lin MINGXI ; Zhang YANDI ; Lin XIAOSONG ; Yao ZONGJIE ; Sheng HUIMING ; Sun ZIYONG ; Wang FENG ; Fan XIONGLIN ; Tao SHENG-CE
Genomics, Proteomics & Bioinformatics 2021;19(5):669-678
Coronavirus disease 2019(COVID-19),which is caused by SARS-CoV-2,varies with regard to symptoms and mortality rates among populations.Humoral immunity plays critical roles in SARS-CoV-2 infection and recovery from COVID-19.However,differences in immune responses and clinical features among COVID-19 patients remain largely unknown.Here,we report a database for COVID-19-specific IgG/IgM immune responses and clinical parameters(named COVID-ONE-hi).COVID-ONE-hi is based on the data that contain the IgG/IgM responses to 24 full-length/truncated proteins corresponding to 20 of 28 known SARS-CoV-2 proteins and 199 spike protein peptides against 2360 serum samples collected from 783 COVID-19 patients.In addition,96 clinical parameters for the 2360 serum samples and basic information for the 783 patients are integrated into the database.Furthermore,COVID-ONE-hi provides a dashboard for defining samples and a one-click analysis pipeline for a single group or paired groups.A set of samples of interest is easily defined by adjusting the scale bars of a variety of parameters.After the"START"button is clicked,one can readily obtain a comprehensive analysis report for further interpretation.COVID-ONE-hi is freely available at www.COVID-ONE.cn.
9. Imaging dynamic observation of COVID-19 patients cured by imported coronavirus pneumonia
Xiaohu LI ; Haitao WANG ; Juan ZHU ; Xiaohui QIU ; Jinping ZHANG ; Guoquan HUANG ; Xiaosong ZENG ; Kewu HE ; Zongyu XIE ; Qizhong XU ; Bin LIU ; Yongqiang YU
Chinese Journal of Radiology 2020;54(0):E012-E012
Objective:
To explore the imaging changes of lung lesions in patients with imported COVID-19 patients when reaching the discharge standard.
Method:
The clinical and CT imaging data of 60 patients with imported COVID-19 cured and discharged from January to February 2020 in Anhui Province were retrospectively collected. The clinical characteristics of the patients and the characteristics of chest CT images at discharge were analyzed.
Results:
Fever (57 cases) and cough (55 cases) were the main symptoms in 60 patients. At the initial diagnosis, 5 cases were mild, 53 were ordinary, and 2 were severe. In 5 light patients, 3 cases were negative in the whole course of CT examination, 2 cases were negative in the first time and abnormal in the second time. . The first CT imaging features of 55 patients (53 common type and 2 severe type)were mainly bilateral lung involvement (51 cases), multiple lesions (33 cases), more common under the pleura (40 cases), and ground glass opacities were the most common. (55 cases). The clinical features of chest CT in clinical outcomes are that the ground glass shadow in the lung gradually fades and was completely absorbed (19 cases); the scope of ground glass shadow in the lung expanded and progressed to crazy-paving, consolidation shadow, and the lesion gradually absorbs again followed by Fibrous cord shadows (27 cases); ground-glass opacities in the lungs quickly progressed to a consolidation and then slowly absorbed . Most of the lesions were accompanied by more residual fibrous cord shadows (4 cases). In 2 severe patients, the lesions in the lungs were larger ground glass, and a big amount of fibrous foci remained after slowly absorption.
Conclusion
Chest CT plays an important role in the diagnosis and treatment of imported COVID-19, and the degree of lung involvement seen on CT images is in good agreement with clinical outcome.
10.Imaging dynamic observation of cured COVID-19 patients with imported coronavirus pneumonia
Xiaohu LI ; Haitao WANG ; Juan ZHU ; Xiaohui QIU ; Jinping ZHANG ; Guoquan HUANG ; Xiaosong ZENG ; Kewu HE ; Zongyu XIE ; Qizhong XU ; Bin LIU ; Yongqiang YU
Chinese Journal of Radiology 2020;54(5):435-439
Objective:To explore the imaging changes of lung lesions in patients with imported COVID-19 when reaching the discharge standard.Methods:The clinical and CT imaging data of 60 cured patients with imported COVID-19 and discharged from January to February 2020 in Anhui Province were retrospectively collected. At the initial diagnosis, 5 cases were mild, 53 were ordinary, and 2 were severe. The clinical characteristics of the patients and the characteristics of chest CT images at discharge were analyzed.Results:Fever (57 cases) and cough (55 cases) were the main symptoms in 60 patients. In 5 mild patients, 3 cases were negative in the whole course of CT examination, 2 cases were negative in the first time and abnormal in the second time. The first CT imaging features of 55 patients (53 common type and 2 severe type) were mainly bilateral lung involvement (51 cases), multiple lesions (33 cases), more common under the pleura (40 cases), and ground glass opacities were the most common (55 cases). The features of chest CT in clinical outcomes were that the ground glass shadow in the lung gradually faded and was completely absorbed (19 cases); the scope of ground glass shadow in the lung expanded and progressed to crazy-paving, consolidation shadow, and the lesion gradually absorbed again followed by fibrous cord shadows (27 cases); ground-glass opacities in the lungs quickly progressed to a consolidation and then slowly absorbed. Most of the lesions were accompanied by more residual fibrous cord shadows (4 cases). In 2 severe patients, the lesions in the lungs were larger ground glass, and a large amount of fibrous foci remained after slow absorption.Conclusions:Chest CT plays an important role in the diagnosis and treatment of imported COVID-19, and the degree of lung involvement seen on CT images is in good agreement with clinical outcome.

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