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REDH:A database of RNA editome in hematopoietic differentiation and malignancy

Chinese Medical Journal 2024年第3期137卷 283-293页

作者： Jiayue Xu Jiahuan He Jiabin Yang Fengjiao Wang Yue Huo Yuehong Guo Yanmin Si Yufeng Gao Fang Wang Hui Cheng Tao Cheng Jia Yu Xiaoshuang Wang Yanni Ma State Key Laboratory of Common Mechanism Research for Major Diseases Haihe Laboratory of Cell EcosystemInstitute of Basic Medical SciencesChinese Academy of Medical SciencesBeijing 100005China Key Laboratory of RNA and Hematopoietic Regulation Chinese Academy of Medical SciencesBeijing 100005China Department of Biochemistry and Molecular Biology Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijing 100005China State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood DiseasesInstitute of Hematology and Blood Diseases HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeTianjin 300020China Institute of blood Transfusion Chinese Academy of Medical SciencesChengduSichuan 610052China

Background:The conversion of adenosine(A)to inosine(I)through deamination is the prevailing form of RNA editing,impacting numerous nuclear and cytoplasmic transcripts across various eukaryotic *** of high-confidence RNA editing sites have been identified and integrated into various RNA databases,providing a convenient platform for the rapid identification of key drivers of cancer and potential therapeutic ***,the available database for integration of RNA editing in hematopoietic cells and hematopoietic malignancies is still ***:We downloaded RNA sequencing(RNA-seq)data of 29 leukemia patients and 19 healthy donors from National center for Biotechnology Information(NCBI)Gene Expression Omnibus(GEO)database,and RNA-seq data of 12 mouse hematopoietic cell populations obtained from our previous research were also *** performed sequence alignment,identified RNA editing sites,and obtained characteristic editing sites related to normal hematopoietic development and abnormal editing sites associated with hematologic ***:We established a new database,"REDH",represents RNA editome in hematopoietic differentiation and *** is a curated database of associations between RNA editome and *** integrates 30,796 editing sites from 12 murine adult hematopoietic cell populations and systematically characterizes more than 400,000 edited events in malignant hematopoietic samples from 48 cohorts(human).Through the Differentiation,Disease,Enrichment,and knowledge modules,each A-to-I editing site is systematically integrated,including its distribution throughout the genome,its clinical information(human sample),and functional editing sites under physiological and pathological ***,REDH compares the similarities and differences of editing sites between different hematologic malignancies and healthy ***:REDH is accessible at http://***/.This user-friendly database

关键词： RNA editing Hematopoietic differentiation Hematopoietic malignancy Database management systems

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Naked-eye visualization of lymph nodes using fluorescence nanoprobes in non-human primate-animal models

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Nano Research 2024年第8期17卷 7404-7414页

作者： Xiaoyuan Ji Binbin Chu Xiaofeng Wu Zhiming Xia Airui Jiang Chenyu Wang Zhiming Chen Danni Zhong Qiaolin Wei Bin Song Wanlin Li Yiling Zhong Houyu Wang Fenglin Dong Min Zhou Yao He suzhou Key Laboratory of Nanotechnology and Biomedicine Jiangsu Key Laboratory for Carbon-Based Functional Materials&DevicesInstitute of Functional Nano and Soft Materials(FUNSOM)Soochow UniversitySuzhou 215123China School of Public Health Shanghai Jiao Tong University School of MedicineShanghai 200025China Zhejiang University-University of Edinburgh Institute(ZJU-UoE Institute) Zhejiang UniversityHaining 314400China Department of Ultrasound the First Affiliated Hospital of Soochow UniversitySuzhou 215006China State Key Laboratory(SKL)of Biobased Transportation Fuel Technology Zhejiang UniversityHangzhou 310027China School of Pharmacy Hangzhou Normal UniversityHangzhou 311121China Macao Translational Medicine center Macao University of Science and TechnologyTaipa 999078MacaoChina Macao Institute of Materials Science and Engineering Macao University of Science and TechnologyTaipa 999078MacaoChina

Despite sufficient studies performed in non-primate animal models,there exists scanty information obtained from pilot trials in non-human primate animal models,severely hindering nanomaterials moving from basic research into clinical *** herein present a pioneering demonstration of nanomaterials based optical imaging-guided surgical operation by using macaques as a typical kind of non-human primate-animal ***,taking advantages of strong and stable fluorescence of the small-sized(diameter:~5 nm)silicon-based nanoparticles(SiNPs),lymphatic drainage patterns can be vividly visualized in a real-time manner,and lymph nodes(LN)are able to be sensitively detected and precisely excised from small animal models(e.g.,rats and rabbits)to non-human primate animal models(e.g.,cynomolgus macaque(Macaca fascicularis)and rhesus macaque(Macaca mulatta)).Compared to clinically used invisible near-infrared(NIR)lymphatic tracers(i.e.,indocyanine green(ICG);etc.),we fully indicate that the SiNPs feature unique advantages for naked-eye visible fluorescence-guided surgical operation in long-term *** toxicological analysis in macaque models further provides confirming evidence of favorable biocompatibility of the SiNPs *** expect that our findings would facilitate the translation of nanomaterials from the laboratory to the clinic,especially in the field of cancer treatment.

关键词： fluorescent silicon nanoparticles lymph node real-time naked-eye visualization macaque models

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Analysis of the Efficacy of Xuebijing Combined with Antimicrobials in the Treatment of Intensive Care Unit Patients with Severe Pneumonia

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Journal of Clinical and Nursing Research 2024年第6期8卷 123-128页

作者： Han Zou Yuting Song Jiaju Ma Hebu Qian Yueping Yao suzhou Ninth People's Hospital Suzhou 215200Jiangsu ProvinceChina

Objective:To analyze the therapeutic effect of Xuebijing+antimicrobials in intensive care unit(ICU)patients with severe ***:60 ICU patients with severe pneumonia from June 2021 to June 2023 were selected and divided by the random number table method,with 30 cases in each *** observation group received Xuebijing+antimicrobial treatment,while the control group received only antimicrobial *** differences in rehabilitation indexes,test indexes,and inflammation indexes were compared between the two ***:Mechanical ventilation time,fever reduction time,cough relief time,and hospitalization time of the observation group were significantly shorter than those of the control group(Pblood cell count of the observation group were significantly lower than those of the control group(P<0.05);interleukin-6 and tumor necrosis factor-aαof the observation group were significantly lower than those of the control group(P<0.05).Conclusion:The treatment of severe pneumonia patients in ICU with Xuebijing+antibacterial drugs can reduce inflammation,enhance immune function,shorten the pneumonia recovery time,and reduce the adverse reactions of severe pneumonia.

关键词： Intensive care unit severe pneumonia Antimicrobials Xuebijing Efficacy

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Transfer learning enhanced graph neural network for aldehyde oxidase metabolism prediction and its experimental application

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Acta Pharmaceutica Sinica B 2024年第2期14卷 623-634页

作者： Jiacheng Xiong Rongrong Cui Zhaojun Li Wei Zhang Runze Zhang Zunyun Fu Xiaohong Liu Zhenghao Li Kaixian Chen Mingyue Zheng Drug Discovery and Design center State Key Laboratory of Drug ResearchShanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China University of Chinese Academy of Sciences Beijing 100049China College of Computer and Information Engineering Dezhou UniversityDezhou 253023China AI Department Suzhou Alphama Biotechnology Co.Ltd.Suzhou 215000China Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and TechnologyShanghaiTech UniversityShanghai 200031China State Key Laboratory of Pharmaceutical Biotechnology Nanjing UniversityNanjing 210023China

Aldehyde oxidase(AOX)is a molybdoenzyme that is primarily expressed in the liver and is involved in the metabolism of drugs and other ***-mediated metabolism can result in unexpected outcomes,such as the production of toxic metabolites and high metabolic clearance,which can lead to the clinical failure of novel therapeutic *** models can assist medicinal chemists in rapidly evaluating the AOX metabolic risk of compounds during the early phases of drug discovery and provide valuable clues for manipulating AOX-mediated metabolism *** this study,we developed a novel graph neural network called AOMP for predicting AOX-mediated *** integrated the tasks of metabolic substrate/non-substrate classification and metabolic site prediction,while utilizing transfer learning from 13C nuclear magnetic resonance data to enhance its performance on both *** significantly outperformed the benchmark methods in both cross-validation and external *** AOMP,we systematically assessed the AOX-mediated metabolism of common fragments in kinase inhibitors and successfully identified four new scaffolds with AOX metabolism liability,which were validated through in vitro ***,for the convenience of the community,we established the first online service for AOX metabolism prediction based on AOMP,which is freely available at https://***.

关键词： Drugmetabolism Aldehyde oxidase Transferlearning Graph neural network Kinase inhibitor

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Visible-light-driven photocatalysis degradation of antibiotic pollutants by La-doped CeO2 nanorods:synergy of La doping and oxygen vacancy

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Rare Metals 2024年第7期43卷 3134-3145页

作者： Shi-Hai Cao Jing-Ru Qu Yu-Qi Zhao Yun-Tong Sun Wen-Tong Gao Bing Han Yao Lu College of Environmental Engineering Nanjing Institute of Technology School of Materials Science and Engineering Nanjing Institute of Technology School of Chemistry Chemical Engineering and BiotechnologyNanyang Technological University Institute of Environmental Health and Ecological Security School of Environment and Safety EngineeringJiangsu University Jiangsu Collaborative Innovation center of Technology and Material of Water Treatment Suzhou University of Science and Technology

Elemental doping is an effective strategy to enhance photocatalytic activity and extend the light absorption range of single-component *** this work,a series of La-doped CeO2nanorods（La-CeO2-x） with La content of 1 wt%-15 wt% are synthesized by a simple hydrothermal method and further used as photocatalyst for sulfamerazine（SMR） *** prepared La-CeO2-x nanorods exhibit a great improvement in electron-hole pair migration and visible-light response due to the synergistic effect of abundant oxygen vacancies and heterogeneous elements（La）.Consequently,La-CeO2-x exhibited excellent visible-light photocatalytic performances and chemical stability for SMR degradation,the La-CeO2-5 sample achieved the highest SMR degradation rate of 81%,which was 3.4 times higher than that of the original ***,three possible degradation pathways of SMR in La-CeO2photocatalytic reactions were proposed by liquid chromatography-mass spectrometry ***,density functional theory calculations were carried out to provide an in-depth understanding of the structure-performance *** its excellent properties and better photocatalytic performance,this study demonstrates that La doping in CeO2is an effective way to increase oxygen vacancy and improve the photochemical properties of photocatalysts.

关键词： CeO 2 nanorod La-doped Photocatalysis Oxygen vacancy Sulfamerazine

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Transfer-free chemical vapor deposition graphene for nitride epitaxy: challenges, current status and future outlook

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Science China Chemistry 2024年第3期67卷 824-840页

作者： Xiang Gao Senlin Li Jingfeng Bi Kaixuan Zhou Meng Li Zhongfan Liu Jingyu Sun College of Energy Soochow Institute for Energy and Materials InnovationsSUDA-BGI Collaborative Innovation CenterKey Laboratory of Advanced Carbon Materials and Wearable Energy Technologies of Jiangsu ProvinceSoochow UniversitySuzhou 215006China Beijing Graphene Institute Beijing 100095China Xiamen Silan Advanced Compound Semiconductor Co.Ltd. Xiamen 361026China

Graphene, a two-dimensional material with outstanding electrical and mechanical properties, has attracted considerable attention in the field of semiconductor technologies due to its potential use as a buffer layer for the epitaxial Ⅲ-nitride growth. In recent years, significant progress has been made in the chemical vapor deposition growth of graphene on various insulating substrates for the nitride epitaxy, which offers a facile, inexpensive, and easily scalable methodology. However, certain challenges are still present in the form of producing high-quality graphene and achieving optimal interface compatibility with Ⅲ-nitride *** this review, we provide an overview of the bottlenecks associated with the transferred graphene fabrication techniques and the state-of-the-art techniques for the transfer-free graphene growth. The present contribution highlights the current progress in the transfer-free graphene growth on different insulating substrates, including sapphire, quartz, SiO_(2)/Si, and discusses the potential applications of transfer-free graphene in the Ⅲ-nitride epitaxy. Finally, it includes the prospects of the transfer-free graphene growth for the Ⅲ-nitride epitaxy and the challenges that should be overcome to realize its full potential in this field.

关键词： Transfer-free chemical vapor deposition graphene for nitride epitaxy challenges current status and future outlook graphene

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Thiol-Disulfide Exchange Coordinates the Release of Nitric Oxide and Dexamethasone for Synergistic Regulation of Intestinal Microenvironment in Colitis

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Research 2024年第2期6卷 285-300页

作者： Junna Lu Tongfei Shi Chengxin Shi Fangman Chen Chao Yang Xiaochun Xie Zheng Wang He Shen Jiaqi Xu Kam W.Leong Dan Shao School of Biomedical Sciences and Engineering South China University of TechnologyGuangzhou International CampusGuangzhouGuangdong 510006China National Engineering Research center for Tissue Restoration and Reconstruction South China University of TechnologyGuangdong 510006China Department of Plastic and Aesthetic center The First Affliated Hospital of Zhejiang UniversityHangzhou 310000China Department of Biomedical Engineering Columbia UniversityNew YorkNY 10027USA School of Medicine South China University of TechnologyGuangzhouGuangdong 510006China CAS Key Laboratory of Nano-Bio Interface Suzhou Institute of Nano-Tech and NanoBionicsChinese Academy of SciencesSuzhou 215123China CAS Key Laboratory for Biomedical Efects of Nanomaterials&Nanosafety CAS Center for Excellence in NanoscienceNational Center for Nanoscience and TechnologyBeijing 100190China Guangdong Provincial Key Laboratory of Biomedical Engineering South China University of TechnologyGuangzhou 510006China Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education South China University of TechnologyGuangzhou 510006China

The cell-specific functions of nitric oxide(NO)in the intestinal microenvironment orchestrate its therapeutic effects in ulcerative *** most biomaterials show promise by eliciting the characteristics of NO,the insufficient storage,burst release,and pro-inflammatory side effects of NO remain as ***,we report the development of thiol-disulfide hybrid mesoporous organosilica nanoparticles(MONs)that improve the storage and sustained release of NO,broadening the therapeutic window of NO-based therapy against *** tailored NO-storing nanomaterials coordinated the release of NO and the immunoregulator dexamethasone(Dex)in the intestinal microenvironment,specifically integrating the alleviation of oxidative stress in enterocytes and the reversal of NO-exacerbated macrophage ***,such a synchronous operation was achieved by a self-motivated process wherein the thiyl radicals produced by NO release cleaved the disulfide bonds to degrade the matrix and release Dex via thiol-disulfide ***,the MON-mediated combination of NO and Dex greatly ameliorated intractable colitis compared with 5-aminosalicylic acid,even after delayed ***,our results reveal a key contribution of synergistic modulation of the intestinal microenvironment in NO-based colitis therapy and introduce thiol-disulfide hybrid nanotherapeutics for the management of inflammatory diseases and cancer.

关键词： sustained release disulfide

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Effect of frequent blood pressure measurements after discharge on clinical outcomes in ischemic stroke patients

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Chinese Medical Journal 2024年第13期137卷 1629-1631页

作者： Ruirui Wang Yanni Wu Mengyao Shi Pinni Yang Yang Liu Yang Jiao Yanbo Peng Aili Wang Tan Xu Jing Chen Yonghong Zhang Jiang He Department of Epidemiology School of Public Health and Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric DiseasesSuzhou Medical College of Soochow UniversitySuzhouJiangsu 215123China Department of Cardiology Second Affiliated Hospital of Soochow UniversitySuzhouJiangsu 215004China Department of Epidemiology Tulane University School of Public Health and Tropical MedicineNew OrleansLA 70112USA Department of Cardiology First Affiliated Hospital of Soochow UniversitySuzhouJiangsu 215129China Department of Neurology Affiliated Hospital of North China University of Science and TechnologyTangshanHebei 063000China Department of Medicine Tulane University School of MedicineNew OrleansLA 70112USA

To the Editor:Stroke is a major cause of death and longterm serious disability in adults *** is the most important modifiable risk factor for primary and secondary prevention of stroke.[1]Even a modest reduction in clinical blood pressure(BP)of approximately 10/5 mmHg is associated with a significant 30%risk reduction of adverse clinical *** clinical evidence strongly advocated the effectiveness of managing BP to reduce adverse outcomes after ischemic stroke,[2]the management and control of BP in ischemic stroke patients after discharge remain poor.

关键词： prevention death after

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Mass spectrometry analysis of intact protein N-glycosylation signatures of cells and sera in pancreatic adenocarcinomas

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2024年第1期25卷 51-64页

作者： Mingming XU Zhaoliang LIU Wenhua HU Ying HAN Zhen WU Sufeng CHEN Peng XIA Jing DU Xumin ZHANG Piliang HAO Jun XIA Shuang YANG center for Clinical Mass Spectrometry College of Pharmaceutical SciencesSoochow UniversitySuzhou215123China School of Life Science and Technology ShanghaiTech UniversityShanghai201210China State Key Laboratory of Genetic Engineering Department of BiochemistrySchool of Life SciencesFudan UniversityShanghai200438China Department of Clinical Laboratory center Zhejiang Provincial People’s HospitalPeople’s Hospital of Hangzhou Medical CollegeHangzhou310014China

Pancreatic cancer is among the most malignant cancers,and thus early intervention is the key to better survival ***,no methods have been derived that can reliably identify early precursors of development into ***,it is urgent to discover early molecular changes during pancreatic *** aberrant glycosylation is closely associated with cancer progression,numerous efforts have been made to mine glycosylation changes as biomarkers for diagnosis;however,detailed glycoproteomic information,especially site-specific N-glycosylation changes in pancreatic cancer with and without drug treatment,needs to be further ***,we used comprehensive solid-phase chemoenzymatic glycoproteomics to analyze glycans,glycosites,and intact glycopeptides in pancreatic cancer cells and patient *** profiling of N-glycans in cancer cells revealed an increase in the secreted glycoproteins from the primary tumor of MIA PaCa-2 cells,whereas human sera,which contain many secreted glycoproteins,had significant changes of glycans at their specific *** results indicated the potential role for tumor-specific glycosylation as disease *** also found that AMG-510,a small molecule inhibitor against Kirsten rat sarcoma viral oncogene homolog(KRAS)G12C mutation,profoundly reduced the glycosylation level in MIA PaCa-2 cells,suggesting that KRAS plays a role in the cellular glycosylation process,and thus glycosylation inhibition contributes to the anti-tumor effect of AMG-510.

关键词： Pancreatic cancer Glycosylation Biomarker Glycoproteomics Mass spectrometry

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Neuropathological characteristics of abnormal white matter functional signaling in adolescents with major depression

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World Journal of Psychiatry 2024年第2期14卷 276-286页

作者： Xin-Lin Huang Ju Gao Yong-Ming Wang Feng Zhu Jing Qin Qian-Nan Yao Xiao-Bin Zhang Hong-Yan Sun Imaging and Nuclear Medicine Jiamusi UniversityJiamusi 154000Heilongjiang ProvinceChina Department of Psychiatry The Affiliated Guangji Hospital of Soochow UniversitySuzhou 215137Jiangsu ProvinceChina School of Biology&Basic Medical Sciences Medical College of Soochow UniversitySuzhou 215137Jiangsu ProvinceChina Department of Radiology Shanghai Anting HospitalShanghai 20000China Department of Radiology The Affiliated Guangji Hospital of Soochow UniversitySuzhou 215137Jiangsu ProvinceChina

BACKGROUND Major depression disorder(MDD)constitutes a significant mental health *** surveys indicate that the lifetime prevalence of depression in adolescents is much higher than that in adults,with a corresponding increased risk of *** studying brain dysfunction associated with MDD in adolescents,research on brain white matter(WM)is *** researchers even mistakenly regard the signals generated by the WM as noise *** fact,studies have shown that WM exhibits similar blood oxygen level-dependent signal *** alterations in WM signals and their relationship with disease severity in adolescents with MDD remain *** To explore potential abnormalities in WM functional signals in adolescents with *** This study involved 48 adolescent patients with MDD and 31 healthy controls(HC).All participants were assessed using the Patient Health Questionnaire-9 Scale and the mini international neuropsychiatric interview(MINI)suicide *** addition,a Siemens Skyra 3.0T magnetic resonance scanner was used to obtain the subjects'image *** DPABI software was utilized to calculate the WM signal of the fractional amplitude of low frequency fluctuations(fALFF)and regional homogeneity,followed by a two-sample t-test between the MDD and HC *** component analysis(ICA)was also used to evaluate the WM functional ***’s correlation was performed to assess the relationship between statistical test results and clinical *** Compared to HC,individuals with MDD demonstrated a decrease in the fALFF of WM in the corpus callosum body,left posterior limb of the internal capsule,right superior corona radiata,and bilateral posterior corona radiata[P<0.001,family-wise error(FWE)voxel correction].The regional homogeneity of WM increased in the right posterior limb of internal capsule and left superior corona radiata,and decreased in the left superior longitudinal fasciculus(P<0.001,FWE voxel corre

关键词： White matter Regional homogeneity The fractional amplitude of low-frequency fluctuations Independent component analysis Adolescents Major depression disorders

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