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DeeReCT-APA:Prediction of Alternative Polyadenylation Site Usage Through Deep Learning

Genomics, Proteomics & Bioinformatics 2022年第3期20卷 483-495页

作者： Zhongxiao Li Yisheng Li Bin Zhang yu Li Yongkang Long Juexiao Zhou Xudong Zou min Zhang yuhui Hu Wei Chen Xin Gao King Abdullah University of Science and Technology(KAUST) Computational Bioscience Research Center(CBRC)ComputerElectrical and Mathematical Sciences and Engineering(CEMSE)DivisionThuwal 23955-6900Saudi Arabia Department of Biology Southern University of Science and Technology(SUSTech)Shenzhen 518055China Cancer Science Institute of Singapore Singapore 117599Singapore

Alternative polyadenylation(APA)is a crucial step in post-transcriptional *** bioinformatic studies have mainly focused on the recognition of polyadenylation sites(PASs)in a given genomic sequence,which is a binary classification ***,computational methods for predicting the usage level of alternative PASs in the same gene have been ***,all of them cast the problem as a non-quantitative pairwise comparison task and do not take the competition among multiple PASs into *** address this,here we propose a deep learning architecture,Deep Regulatory Code and Tools for Alternative Polyadenylation(DeeReCT-APA),to quantitatively predict the usage of all alternative PASs of a given *** accommodate different genes with potentially different numbers of PASs,DeeReCT-APA treats the problem as a regression task with a variable-length *** on a convolutional neural network-long short-term memory(CNN-LSTM)architecture,DeeReCT-APA extracts sequence features with CNN layers,uses bidirectional LSTM to explicitly model the interactions among competing PASs,and outputs percentage scores representing the usage levels of all PASs of a *** addition to the fact that only our method can quantitatively predict the usage of all the PASs within a gene,we show that our method consistently outperforms other existing methods on three different tasks for which they are trained:pairwise comparison task,highest usage prediction task,and ranking ***,we demonstrate that our method can be used to predict the effect of genetic variations on APA patterns and sheds light on future mechanistic understanding in APA *** code and data are available at https://***/lzx325/DeeReCT-APA-repo.

关键词： Polyadenylation Gene regulation Sequence analysis Deep learning Bioinformatics

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Disinfection and Protective Measures for Makeshift Hospitals

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Biomedical and Environmental Sciences 2020年第12期33卷 940-942页

作者： WANG jia Qi LIU Xiao Li DUAN Hong Yang CHEN Xiao min QIAN Le Lyu Xi Fang CHENG Yi Bin LIANG jian Sheng YAO Xiao yuan National Institute of Environmental Health Chinese Center for Disease Control and PreventionBeijing 100021China Wuhan Center For Disease Control and Prevention Wuhan 430024HubeiChina

During the COVID-19 epidemic,Wuhan city had the hardest hit in *** treatment capacity of the local medical system exceeded due to the rapid growth of COVID-19 *** a result,a considerable part of diagnosed patients could not be admitted to hospitals for isolation and treatment in time,causing the risk of spreading in the *** effectively achieve the goals of controlling the source of infection by cutting off the transmission route,increasing the cure rate and reducing the mortality rate,Wuhan has reconstructed several makeshift hospitals based on large public places.

关键词： China. admitted Wuhan

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Clinically significant endoscopic findings in patients of dyspepsia with no warning symptoms:A cross-sectional study

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World Journal of Clinical Cases 2021年第15期9卷 3597-3606页

作者： Li-Qi Mao Shuang-Shuang Wang Yan-Lin Zhou Lin Chen Lei-min yu Meng Li Bin Lv Department of Gastroenterology The First Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhou 310006Zhejiang ProvinceChina Department of Gastroenterology Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical UniversityTaizhou 317000Zhejiang ProvinceChina Department of Gastroenterology Guangxing Hospital Affiliated to Zhejiang Chinese Medical UniversityHangzhou 310007Zhejiang ProvinceChina

BACKGROUND Dyspepsia is one of the commonest clinical ***,controversy remains over the role of endoscopy in patients with *** studies have evaluated the diagnostic value of endoscopy in patients with no warning symptoms according to the Rome IV *** To study the diagnostic value of endoscopy in dyspeptic patients with no warning *** This cross-sectional study included dyspeptic patients with no warning symptoms who met the inclusion and exclusion criteria at The First Affiliated Hospital,Zhejiang Chinese Medical University from April 2018 to February *** clinical data were collected using questionnaires,including dyspeptic information,warning symptoms,other diseases,family history and basic demographic *** on dyspeptic symptoms,patients can be divided into epigastric pain syndrome,postprandial distress syndrome or overlapping *** A total of 1016 cases were enrolled,304(29.9%)had clinically significant findings that were detectable by *** endoscopy findings included esophageal lesions in 180(17.7%)cases,peptic ulcers in 115(11.3%)cases and malignancy in 9(0.89%)*** logistic regression analysis showed that males[odds ratio(OR)=1.758,P25(OR=1.660;P=0.005),epigastric pain(OR=1.423;P=0.019)and Helicobacter pylori infection(OR=1.949;P25,epigastric pain or Helicobacter pylori infection.

关键词： Rome IV Dyspepsia Questionnaire Endoscopy Warning symptoms Diagnosis

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Therapeutic potential of dental pulp stem cell transplantation in a rat model of Alzheimer’s disease

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Neural Regeneration Research 2021年第5期16卷 893-898页

作者： Xue-Mei Zhang yuan-jiao Ouyang Bing-Qian yu Wei Li Mei-yu yu Jin-yue Li Zhuo-min jiao Dan Yang Na Li Ying Shi yun-yun Xu Zhi-Jun He Duo Wang Hui yue Jin Fu Department of Neurology The 2nd Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiang ProvinceChina Department of Neurology Ningbo Hangzhou Bay HospitalNingboZhejiang ProvinceChina Department of Neurology the First Hospital of QiqiharQiqiharHeilongjiang ProvinceChina

Dental pulp stem cells are dental pulp-derived mesenchymal stem cells that originate from the neural *** exhibit greater potential for the treatment of nervous system diseases than other types of stem cells because of their neurogenic differentiation capability and their ability to secrete multiple neurotrophic *** studies have reported Alzheimer’s disease treatment using dental pulp stem *** models of Alzheimer’s disease were established by injecting amyloid-β1–42 into the *** days later,5×106 dental pulp stem cells were injected into the *** and western blot assays showed that dental pulp stem cell transplantation increased the expression of neuron-related doublecortin,NeuN,and neurofilament 200 in the hippocampus,while the expression of amyloid-βwas ***,cognitive and behavioral abilities were *** findings indicate that dental pulp stem cell transplantation in rats can improve cognitive function by regulating the secretion of neuron-related proteins,which indicates a potential therapeutic effect for Alzheimer’s *** study was approved by the Animal Ethics Committee of Harbin Medical University,China(approval ***2017-132)on February 21,2017.

关键词： Alzheimer’s disease brain central nervous system dental pulp stem cell in vivo model rat stem cells transplantation

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Aspiration pneumonia during general anesthesia induction after esophagectomy: A case report

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World Journal of Clinical Cases 2020年第21期8卷 5409-5414页

作者： jia-Xi Tang Ling Wang Wei-Qi Nian Wan-Yan Tang Jing-yu Xiao Xi-Xi Tang Hong-Liang Liu Department of Anesthesiology Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized TreatmentChongqing University Cancer HospitalChongqing 400030China Department of Phase I Clinical Trial Ward Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized TreatmentChongqing University Cancer HospitalChongqing 400030China

BACKGROUND Esophageal cancer is a common malignant tumor of the digestive *** present,surgery is the most important treatment *** esophagectomy and gastric esophagoplasty,the patients are prone to ***,these patients currently do not receive much attention,especially from *** SUMMARY A 55-year-old woman was scheduled for right lower lung *** patient had undergone radical surgery for esophageal cancer under general anesthesia 6 mo *** the patient had fasted for>17 h,unexpected aspiration still occurred during induction of general *** the operation,oxygen saturation was 98%-100%,but the airway pressure was high(35 cmH2O at double lung ventilation).The patient was sent to the intensive care unit after *** chest radiography was performed,which showed exudative lesions in both lungs compared with the preoperative *** surgery,antibiotics were given to prevent lung *** day 2 in the intensive care unit,the patient was extubated and discharged on postoperative day 7 without complications related to aspiration *** After esophagectomy,patients are prone to *** recommend nasogastric tube placement followed by rapid sequence induction or conscious intubation.

关键词： Aspiration pneumonia Esophagectomy Gastric esophagoplasty Respiratory aspiration General anesthesia Case report

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Cortical regulation of striatal projection neurons and interneurons in a Parkinson's disease rat model

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Neural Regeneration Research 2016年第12期11卷 1969-1975页

作者： jia-jia Wu Si Chen Li-si Ouyang yu jia Bing-bing Liu Shu-hua Mu yu-xin Ma Wei-ping Wang jia-you Wei You-lan Li Zhi Chen Wan-long Lei Department of Anatomy Zhongshan School of MedicineSun Yat-sen University Periodical Center the Third Affiliated HospitalSun Yat-sen University Department of Anesthesiology Guangdong No.2 Provincial People’s HospitalGuangdong Provincial Emergency Hospital Key Laboratory of Optoelectronic Devices and Systems of ministry of Education and Guangdong Province College of Optoelectronic EngineeringShenzhen University

Striatal neurons can be either projection neurons or interneurons, with each type exhibiting distinct susceptibility to various types of brain damage. In this study, 6-hydroxydopamine was injected into the right medial forebrain bundle to induce dopamine depletion, and/or ibotenic acid was injected into the M1 cortex to induce motor cortex lesions. Immunohistochemistry and western blot assay showed that dopaminergic depletion results in significant loss of striatal projection neurons marked by dopamine- and cyclic adenosine monophosphate-regulated phosphoprotein, molecular weight 32 k Da, calbindin, and μ-opioid receptor, while cortical lesions reversed these pathological changes. After dopaminergic deletion, the number of neuropeptide Y-positive striatal interneurons markedly increased, which was also inhibited by cortical lesioning. No noticeable change in the number of parvalbumin-positive interneurons was found in 6-hydroxydopamine-treated rats. Striatal projection neurons and interneurons show different susceptibility to dopaminergic depletion. Further, cortical lesions inhibit striatal dysfunction and damage induced by 6-hydroxydopamine, which provides a new possibility for clinical treatment of Parkinson＇s disease.

关键词： nerve regeneration motor cortex lesions dopaminergic neurons GABAergic neurons Darpp32 calbindin μ-opioid receptor neuropeptide Y parvalbumin neural regeneration

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C-jun N-terminal Kinase-mediated Signaling Is Essential for Staphylococcus Aureus-induced U937 Apoptosis

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Chinese Medical Sciences Journal 2009年第1期24卷 26-29页

作者： jia-he Wang Bo yu Hui-yan Niu Hui Li Yi Zhang Xin Wang Ping He Department of Geriatrics Shengjing HospitalChina Medical University Shenyang 110004 China Department of Neurosurgery Shengjing HospitalChina Medical University Shenyang 110004 China

Objective To investigate the effect of SP600125, a specific c-jun N-terminal protein kinase (JNK) inhibitor, on Staphylococcus aureus (S. aureus)-induced U937 cell death and the underlying mechanism. Methods The human monocytic U937 cells were treated with S. aureus at different time with or without SP600125. Cell apoptosis was analyzed by flow cytometry. JNK, Bax, and caspase-3 activities were detected by Western blotting. Results S. aureus induced apoptosis in cultured U937 cells in a time-dependent manner. Expression of Bax and phospho-JNK significantly increased in S. aureus-treated U937 cells, and the level of activated caspase-3 also increased in a time-dependent manner. Inhibition of JNK with SP600125 significantly inhibited S. aureus-induced apoptosis in U937 cells. Conclusions S. aureus can induce apoptosis in U937 cells by phosphorylation of JNK and activation of Bax and caspase-3. SP600125 protects U937 cells from apoptosis induced by S. aureus via inhibiting the activity of JNK.

关键词： cell apoptosis U937 cells Staphylococcus aureus JNK signaling pathway SP600125

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Effects of Dachaihu Decoction and Its “Prescription Elements” on Intestinal Flora of Nonalcoholic Fatty Liver Disease Model Rats

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World Journal of Traditional Chinese Medicine 2020年第1期6卷 97-105页

作者： Yan Sun min Wang Shu-Jing Zhang yu-Shan Gao Lin Chen Meng-Yao Wu Xin-Lei Zhang Lu Zhou Hui-min yuan Feng-Jie Zheng jian Cui yu-Hang Li School of Traditional Chinese Medicine Beijing University of Chinese MedicineBeijingChina Department of Medicine Columbia University Medical CenterNYUSA

Objective:The study objective was to observe the effect of Dachaihu decoction and its "prescription elements" on intestinal flora of model rats with nonalcoholic fatty liver disease (NAFLD). Materials and Methods:Healthy male Sprague-Dawley rats were randomly divided into the following seven groups (n=105):normal, model, pioglitazone hydrochloride (PH), Shuganlidan, jianpihuatan, Tongfuxiezhuo, and dachaihu decoction (DD). 16SrRNA high-throughput IIlumina sequencing platform was used for sequencing, and bioinformatics analysis of rat intestinal flora was done. Results:Compared with the normal group, rats in the model, PH, Shuganlidan, jianpihuatan, Tongfuxiezhuo,and DD groups showed significant differences in the intestinal microflora structure. The microorganisms that play an important role in the normal group are Ruminococcaceae, Oscillospira, Lactobacillales, Lactobacillaceae, Lactobacillus, bacilli, Ruminococcus, TM7, Spirochaetes,Clostridium, Elusimicrobia, Elusimicrobiaceae, Elusimicrobiales, Lactobacillus helveticus, Lactobacillus reuteri, Elusimicrobium, RF39, and Christensenellaceae;in the model group are Ruminococcus gnavus;in the PH group are Prevotella, Paraprevotellaceae, and Blautia;in the jianpihuatan group are Bacteroidetes, Bacteroidia, Bacteroidales, Roseburia, Rikenellaceae, and?Stridium methylpentosum;in the TongfuXiezhuo group are Bacteroidaceae, Bacteroides, Porphyromonadaceae, Parabacteroide, 4C0d2, Cyanobacteria, YS2, Parabacteroides distasonis,Bacteroides uniformis, Verrucomicrobiaceae, Verrucomicrobiae, Verrucomicrobiales, Akkermansia, Akkermansia muciniphila, Coprobacillus,Parabacteroides gordonii, Blautia producta, and Ruminococcus torques;and in the DD group are Erysipelotrichales, Erysipelotrichi, and Erysipelothrichaceae. Conclusion:The Tongfuxiezhuo prescription elements of the DD significantly improved the intestinal flora of rats with NAFLD, improving the relative abundance of beneficial bacteria in the intestinal flora of NAFLD rat

关键词： Dachaihu decoction intestinal flora nonalcoholic fatty liver disease prescription elements

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Chitin synthase 1 and five cuticle protein genes are involved in serosal cuticle formation during early embryogenesis to enhance eggshells in Nilaparvata lugens

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Insect Science 2022年第2期29卷 363-378页

作者： jia-Bao Lu jian-Sheng Guo Xuan Chen Chen Cheng Xu-Mei Luo Xiao-Ya Zhang Bernard Moussian jian-Ping Chen Jun-min Li Chuan-Xi Zhang State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang ProvinceInstitute of Plant VirologyNingbo UniversityNingboZhejiang ProvinceChina Institute of Insect Science Zhejiang UniversityHangzhouChina School of Medicine Zhejiang UniversityHangzhouChina UniversitéCôte d'Azur CNRSInsermInstitute of Biology ValroseNiceFrance

Many holo-and hemimetabolous insects enhance their eggshells during embryogenesis by forming a serosal cuticle(SC).To date,scholarly understanding of the SC composition and SC-related gene functions has been limited,especially for hemimetabolous *** this study,we initially performed transmission electron microscopic(TEM)observation and chitin staining of the SC in Nilaparvata lugens,a hemimetabolous rice pest known as the brown planthopper(BPH).We confirmed that the SC was a chitin-rich lamellar structure deposited gradually during the early *** RNA interference(RNAi)against Nilaparvata lugens chitin synthase 1(NlCHS1)in newly emerged and matured females resulted in decreases of egg hatchability by 100%and 76%,*** analyses revealed loss of the lamellar structure of the SC in dsNlCHS1-treated *** to temporal expression profiles,five cuticle protein coding genes,NlugCpr1/2/3/8/90,were specifically or highly expressed during the SC formation period,and NlugCpr1/2/3/90 were further detected in 72 h eggshells extract by ultra-performance liquid chromatography-tandem mass spectrometry/mass ***2/3/90 were likely three SC-specific cuticle *** observations of the SC following parental RNAi against NlugCpr1/2/3/8/90 demonstrated that NlugCpr3/8/90 were essential for SC *** study provided an understanding of the SC formation process and SC-related cuticle proteins in BPHs,which offer potential targets for pest control in the egg stage as well.

关键词： chitin synthase 1 cuticle protein eggshell embryogenesis Nilaparvata lugens serosal cuticle

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Effect of the micro vortex generator on the characteristics of vaporized RP-3 kerosene combustion in supersonic flows

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Journal of Zhejiang University-Science A(Applied Physics & Engineering) 2022年第5期23卷 405-414页

作者： Dong-peng jia Kai YANG yu PAN Xi-peng LI Ning WANG Science and Technology on Scramjet Laboratory College of Aerospace Science and EngineeringNational University of Defense TechnologyChangsha 410073China

To investigate the characteristics of vaporized RP-3 kerosene combustion in a scramjet combustor enhanced by the micro vortex generator(MVG),a series of experiments are carried out based on the advanced combustion diagnosis *** high-enthalpy incoming flow is accelerated to supersonic through a Mach 2.52 nozzle,the total pressure and temperature of which are 1.6 MPa and 1486 K,*** effect of MVG on the ignition process,flame distribution,and combustor pressure along the bottom wall is well revealed,and the effects of the position and number of MVGs on stable combustion performance are *** results indicate that the development processes of the initial flame kernel with and without an MVG during ignition process show a similar *** installation of an MVG can lift the shear layer,promote the penetration of flame deeper into the mainstream,and expand the area of the reactive *** the distance between the MVG and the injection position and increasing the number of MVGs are regarded as effective ways of improving the mixing degree of fuel and air with a resultant intensification of chemical reactions and flame *** effect of mixing and subsequent combustion is enhanced by shortening the distance between the MVG and the injection *** the layout schemes of the MVG vary,the pressure distribution between the injection position and the leading edge of the cavity changes considerably,while that in the cavity remains almost *** the number of MVGs is also beneficial for improving the premixed degree of fuel and incoming flow and results in more violent chemical reactions downstream of the cavity.

关键词： Vaporized RP-3 kerosene Micro vortex generator(MVG) Ignition process Cavity-stabilized flame

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