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Machine learning and bioinformatics to identify biomarkers in response to Burkholderia pseudomallei infection in mice

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BIOCELL 2024年第4期48卷 613-621页

作者： YAO FANG FEI XIA feifei TIAN L EI QU FANG YANG JUAN FANG ZHENHONG HU HAICHAO LIU Department of Respiratory and Critical Care Medicine General Hospital of Center Theater of PLAWuhan430070China School of Medicine Wuhan University of Science and TechnologyWuhan430065China School of Life Science and Engineering Southwest Jiaotong UniversityChengdu611756China

Objective:In the realm of Class I pathogens,Burkholderia pseudomallei(BP)stands out for its propensity to induce severe *** the intricate interactions between BP and host cells is imperative for comprehending the dynamics of BP infection and discerning biomarkers indicative of the host cell response ***:mRNA extraction from BP-infected mouse macrophages constituted the initial step of our *** gene expression arrays,the extracted RNA underwent conversion into digital *** percentile shift method facilitated data processing,with the identiﬁcation of genes manifesting signiﬁcant differences accomplished through the application of the ***,a comprehensive analysis involving Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway was conducted on the differentially expressed genes(DEGs).Leveraging the ESTIMATE algorithm,gene signatures were utilized to compute risk scores for gene expression *** vector machine analysis and gene enrichment scores were instrumental in establishing correlations between biomarkers and macrophages,followed by an evaluation of the predictive power of the identiﬁed ***:The functional and pathway associations of the DEGs predominantly centered around G protein-coupled receptors.A noteworthy positive correlation emerged between the blue module,consisting of 416 genes,and the ***4,identiﬁed through support vector machine analysis among intersecting genes,indicated a robust interaction with macrophages,suggesting its potential as a robust ***4 exhibited commendable predictive efﬁcacy,with BP infection inducing its expression in both macrophages and mouse lung *** blotting in macrophages conﬁrmed a signiﬁcant upregulation of FZD4 expression from 0.5 to 24 h *** mouse lung tissue,FZD4 manifested higher expression in the cytoplasm of pulmonary epithelial cells in BP-infected lungs than in the

关键词： Burkholderia pseudomallei Microarray assay Machine learning Bioinformatics FZD4

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Melatonin improves synapse development by PI3K/Akt signaling in a mouse model of autism spectrum disorder

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Neural Regeneration Research 2024年第7期19卷 1618-1624页

作者： Luyi Wang Man Xu Yan Wang feifei Wang Jing Deng Xiaoya Wang Yu Zhao Ailing Liao Feng Yang Shali Wang Yingbo Li Institute of Neuroscience Department of PhysiologySchool of Basic Medical ScienceChongqing Medical UniversityChongqingChina Department of Pediatric Chongqing University Fuling HospitalChongqingChina Department of Neurosurgery Xinqiao HospitalArmy Medical UniversityChongqingChina Department of Pathology Affiliated Hospital of North Sichuan Medical CollegeNanchongSichuan ProvinceChina NHC Key Laboratory of Birth Defects and Reproductive Health Chongqing Population and Family Planning Science and Technology Research InstituteChongqingChina China National Clinical Research Center for Neurological Diseases Beijing Tiantan HospitalCapital Medical UniversityBeijingChina Advanced Innovation Center for Human Brain Protection Capital Medical UniversityBeijingChina

Autism spectrum disorders are a group of neurodevelopmental disorders involving more than 1100 genes,including Ctnnd2 as a candidate ***2knockout mice,serving as an animal model of autis m,have been demonstrated to exhibit decreased density of dendritic *** role of melatonin,as a neuro hormone capable of effectively alleviating social interaction deficits and regulating the development of dendritic spines,in Ctnnd2 deletion-induced nerve injury remains unclea *** the present study,we discove red that the deletion of exon 2 of the Ctnnd2 gene was linked to social interaction deficits,spine loss,impaired inhibitory neurons,and suppressed phosphatidylinositol-3-kinase(PI3K)/protein kinase B(Akt) signal pathway in the prefrontal *** findings demonstrated that the long-term oral administration of melatonin for 28 days effectively alleviated the aforementioned abnormalities in Ctnnd2 gene-knockout ***,the administration of melatonin in the prefro ntal cortex was found to improve synaptic function and activate the PI3K/Akt signal pathway in this *** pharmacological blockade of the PI3K/Akt signal pathway with a PI3K/Akt inhibitor,wo rtmannin,and melatonin receptor antagonists,luzindole and 4-phenyl-2-propionamidotetralin,prevented the melatonin-induced enhancement of GABAergic synaptic *** findings suggest that melatonin treatment can ameliorate GABAe rgic synaptic function by activating the PI3K/Akt signal pathway,which may contribute to the improvement of dendritic spine abnormalities in autism spectrum disorders.

关键词： autism Ctnnd2 deletion GABAergic neurons melatonin PI3K/Akt signal pathway prefrontal cortex social behavior spine density synaptic-associated proteins

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Single-cell transcriptome sequencing reveals the mechanism regulating rice plumule development

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The Crop Journal 2024年第3期12卷 688-697页

作者： Mingdong Zhu Meng Zhang Kunyong Huang feifei Lu Hong Wang Shaolu Zhao Yinghong Yu Shaoqing Tang Haining Wu Peisong Hu Xiangjin Wei State Key Laboratory of Rice Biology and Breeding China National Center for Rice ImprovementChina National Rice Research InstituteHangzhou 310006ZhejiangChina b State Key Laboratory of Hybrid Rice Hunan Rice Research InstituteHunan Academy of Agricultural SciencesChangsha 410125HunanChina Hunan Provincial Key Laboratory of Plant Functional Genomics and Developmental Regulation College of BiologyHunan UniversityChangsha 410082HunanChina Hubei University Wuhan 430062HubeiChina

Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ ***,the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17,a popular Chinese indica rice *** 15 cell clusters,13 were assigned to cell types using marker genes and cluster-specific *** genes of multiple cell types were expressed in several clusters,suggesting a complex developmental *** genes for signaling by phytohormones such as abscisic acid were highly expressed in specific *** cis-elements in the promoters of genes specifically expressed in cell clusters were calculated,and some key hormone-related motifs were frequent in certain *** expression patterns of genes involved in rapid seed germination,seedling growth,and development were *** findings enhanced our understanding of cellular diversity and specialization within plumules of rice,a monocotyledonous model crop.

关键词： Rice Plumule Single-cell sequencing Regulatory network

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Microarrow sensor array with enhanced skin adhesion for transdermal continuous monitoring of glucose and reactive oxygen species

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Bio-Design and Manufacturing 2024年第1期7卷 14-30页

作者： Xinshuo Huang Baoming Liang Shantao Zheng feifei Wu Mengyi He Shuang Huang Jingbo Yang Qiangqiang Ouyang Fanmao Liu Jing Liu Hui-jiuan Chen Xi Xie State Key Laboratory of Optoelectronic Materials and Technologies School of Electronics and Information TechnologyGuangdong Province Key Laboratory of Display Material and TechnologySun Yat-Sen UniversityGuangzhou 510006China School of Biomedical Engineering Sun Yat-Sen UniversityShenzhen 518107China Pazhou Lab Guangzhou 510330China The First Affiliated Hospital of Sun Yat-Sen University Guangzhou 510006China

Conventional blood sampling for glucose detection is prone to cause pain and fails to continuously record glucose fluctuations in *** glucose monitoring based on implantable electrodes could induce pain and potential tissue inflammation,and the presence of reactive oxygen species(ROS)due to inflammationmay affect glucose *** technology is less invasive,yet microneedle adhesion with skin tissue is *** this work,we developed a microarrow sensor array(MASA),which provided enhanced skin surface adhesion and enabled simultaneous detection of glucose and H_(2)O_(2)(representative of ROS)in interstitial fluid in *** microarrows fabricated via laser micromachining were modified with functional coating and integrated into a patch of a three-dimensional(3D)microneedle *** to the arrow tip mechanically interlocking with the tissue,the microarrow array could better adhere to the skin surface after penetration into *** MASA was demonstrated to provide continuous in vivo monitoring of glucose and H_(2)O_(2) concentrations,with the detection of H_(2)O_(2) providing a valuable reference for assessing the inflammation ***,the MASA was integrated into a monitoring system using custom *** work provides a promising tool for the stable and reliable monitoring of blood glucose in diabetic patients.

关键词： Microarrow sensor array Glucose sensing Reactive oxygen species sensing Integrated system Continuous monitoring

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Oxidative stress-initiated one-carbon metabolism drives the generation of interleukin-10-producing B cells to resolve pneumonia

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Cellular & Molecular Immunology 2024年第1期21卷 19-32页

作者： Ying Fu Baichao Yu Qi Wang Zhou Lu Hushan Zhang Dan Zhang feifei Luo Ronghua Liu Luman Wang Yiwei Chu Department of Immunology School of Basic Medical SciencesShanghai Key Laboratory of Medical Epigenetics and MetabolismInstitutes of Biomedical SciencesFudan UniversityShanghaiChina Zhongshan Hospital Institute of Clinical Science Zhongshan HospitalShanghaiChina Zhaotong Health Vocational College ZhaotongYunnanChina Department of Digestive Diseases Huashan HospitalFudan UniversityShanghaiChina Shanghai Fifth People’s Hospital Fudan UniversityShanghaiChina

The metabolic reprogramming underlying the generation of regulatory B cells during infectious diseases remains *** a Pseudomonas aeruginosa-induced pneumonia model,we reported that IL-10-producing B cells(IL-10+B cells)play a key role in spontaneously resolving infection-mediated *** cytosolic reactive oxygen species(ROS)during inflammation were shown to drive IL-10+B-cell generation by remodeling one-carbon *** of the enzyme serine hydroxymethyltransferase 1(Shmt1)led to inadequate one-carbon metabolism and decreased IL-10+B-cell ***,increased one-carbon flux elevated the levels of the methyl donor S-adenosylmethionine(SAM),altering histone H3 lysine 4 methylation(H3K4me)at the Il10 gene to promote chromatin accessibility and upregulate Il10 expression in B ***,the one-carbon metabolism-associated compound ethacrynic acid(EA)was screened and found to potentially treat infectious pneumonia by boosting IL-10+B-cell ***,these findings reveal that ROS serve as modulators to resolve inflammation by reprogramming one-carbon metabolism pathways in B cells.

关键词： IL-10-producing B cell Reactive oxygen species One-carbon metabolism H3K4me Pneumonia

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Semi-implantable device based on multiplexed microfilament electrode cluster for continuous monitoring of physiological ions

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Bio-Design and Manufacturing 2024年第1期7卷 88-103页

作者： Shuang Huang Shantao Zheng Mengyi He Chuanjie Yao Xinshuo Huang Zhengjie Liu Qiangqiang Ouyang Jing Liu feifei Wu Hang Gao Xi Xie Hui-jiuan Chen State Key Laboratory of Optoelectronic Materials and Technologies Guangdong Province Key Laboratory of Display Material and TechnologySchool of Electronics and Information TechnologySun Yat-Sen UniversityGuangzhou 510006China Guangdong Provincial Key Laboratory of Sensor Technology and Biomedical Instrument School of Biomedical EngineeringSun Yat-Sen UniversityShenzhen 518107China The First Affiliated Hospital of Sun Yat-Sen University Guangzhou 510080China Pazhou Lab Guangzhou 510335China Institute of Microelectronics of the Chinese Academy of Sciences Beijing 100029China

Modern medicine is increasingly interested in advanced sensors to detect and analyze biochemical *** sensors based on potentiometric methods are a promising platform for monitoring physiological ions in biological *** semi-implantable devices are mainly based on single-parameter *** semi-implantable electrodes for multiparameter sensing have more restrictions on the electrode size due to biocompatibility considerations,but reducing the electrode surface area could potentially limit electrode *** study developed a semi-implantable device system comprising a multiplexed microfilament electrode cluster(MMEC)and a printed circuit board for real-time monitoring of intra-tissue K^(+),Ca^(2+),and Na^(+)*** electrode surface area was less important for the potentiometric sensing mechanism,suggesting the feasibility of using a tiny fiber-like electrode for potentiometric *** MMEC device exhibited a broad linear response(K^(+):2–32 mmol/L;Ca^(2+):0.5–4 mmol/L;Na^(+):10–160 mmol/L),high sensitivity(about 20–45 mV/decade),temporal stability(>2weeks),and good selectivity(>80%)for the above *** vitro detection and in vivo subcutaneous and brain experiment results showed that the MMEC system exhibits good multi-ion monitoring performance in several complex *** work provides a platform for the continuous real-time monitoring of ion fluctuations in different situations and has implications for developing smart sensors to monitor human health.

关键词： Multiplexed microfilament electrode cluster Physiological ion sensing Subcutaneous and brain experiment Wearable platform for multi-ion detection Continuous real-time monitoring system

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Clinical Effectiveness of Dienogest in the Treatment of Endometriosis

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Journal of Clinical and Nursing Research 2024年第8期8卷 232-236页

作者： Qiumin Li feifei Liu Obstetrics Department Shaanxi Provincial People’s HospitalXi’an 710000Shaanxi ProvinceChina

Objective:This paper aims to investigate the efficacy of desogestrel in the treatment of ***:In this study,61 patients with endometriosis in our hospital from January 2023 to December 2023 were selected and divided using the random sampling *** the patients were treated with desogestrel and the pain symptom scores and HDL-C(high-density lipoprotein cholesterol)levels of the patients were compared before and after the *** treatment effects and adverse effects during the administration of the drug were closely ***:After the patients were treated with desogestrel,the effective rate of treatment was as high as 98.36%,and the incidence of adverse reactions during treatment was 6.55%.Compared with the pre-treatment period,the scores of various pain symptoms were significantly reduced and the HDL-C level was improved after treatment,with P<***:Desogestrel showed significant efficacy in the treatment of endometriosis,effectively relieving patients’pain while elevating HDL-C *** addition,the incidence of adverse reactions to this drug is relatively low,which is worth utilizing.

关键词： Endometriosis Adverse reactions Dienogest

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Recent techniques on analyses and characterizations of shale gas and oil reservoir

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Energy Reviews 2024年第2期3卷 31-62页

作者： Yamin Wang Zhenlin Wang Zhengchen Zhang Shanshan Yao Hong Zhang Guoqing Zheng feifei Luo Lele Feng Kouqi Liu Liangliang Jiang Institute of Energy Peking UniversityBeijing100871China Petro China Xinjiang Oilfield Company Karamay834000China School of Mining and Petroleum Engineering University of AlbertaEdmontonAlbertaCanada College of Construction Engineering Jilin UniversityChangchun130061China School of Safety Engineering China University of Mining and TechnologyXuzhouChina Department of Chemical and Petroleum Engineering University of CalgaryCalgaryAlbertaCanada

This article offers a comprehensive review focused on the analysis and characterization of shale reservoirs,unconventional hydrocarbon resources that uniquely serve as both the source reservoir for gas and oil,and the *** analyze and characterize shale reservoirs,pore structure,rock components and rock mechanical properties are three main factors to *** three main factors are necessary for successful field operations in shale *** now,there are various techniques utilized to characterize these three ***,this study delves into the intricacies of shale reservoir's pore structure,rock components and mechanical properties under varying geological conditions,summarizing various techniques utilized to characterize these properties in previous *** study also discusses the role of analytical techniques in understanding the complex interactions between kerogen and the surrounding mineral *** providing a summary of various techniques operated on the mentioned three main factors,this paper supplies the effective and optimal technique on analyzing different properties of shale ***,the paper aims to contribute to more effective resource assessment and production optimization in shale reservoirs,offering insights that have significant implications for the future of unconventional hydrocarbon extraction.

关键词： Shale reservoir Pore structure Rock components Mechanical test Kerogen

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Sensory Evaluation of Freeze-Dried Facial Mask and Analysis of User Profile

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China Detergent & Cosmetics 2024年第3期9卷 41-49页

作者： Qi Rong Chu LiLing Wang feifei Yunnan Botanee Bio-technology Group Co. Ltd.China Yunnan Yunke Characteristic Plant Extraction Laboratory Co. Ltd.China

To thoroughly understand market opportunity of freeze-dried facial mask and deeply get insight of consumers’usage behavior and needs,evaluate sensory feelings of 10 screened commercial freeze-dried facial mask products,group test products according to the differences of sensory attributions via Principal Component Analysis(PCA)and Agglomerative Hierarchical Clustering(AHC),pick up the representative ***-dried facial mask users evaluate satisfaction degree of picked up products and participate survey of usage behavior/*** consumer data by AHC to get consumer segmentations and their *** test results show that,sensory data and consumer data,which is from consumers test of screened representative products by performing PCA and AHC on sensory data,can be verified *** is helpful to understand the needs of consumer segmentations and reason to buy by combining sensory data and consumer test.

关键词： freeze-dried facial mask sensory evaluation consumer satisfaction evaluation PCA AHC user profile

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First total synthesis,antitumor evaluation and target identification of mornaphthoate E:A new tubulin inhibitor template acting on PI3K/Akt signaling pathway

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Acta Pharmaceutica Sinica B 2024年第5期14卷 2177-2193页

作者： Peipei Shan Tao Ye Ying-De Tang Hui Song Chao Wang Kongkai Zhu feifei Yang Shi-Lei Zhang Pei-Wen Su Shuanhu Gao Hua Zhang Institute of Translational Medicine the Affiliated Hospital of Qingdao UniversityCollege of MedicineQingdao UniversityQingdao 266021China School of Biological Science and Technology University of JinanJinan 250022China Advanced Medical Research Institute Cheeloo College of MedicineShandong UniversityJinan 250012China College of Pharmaceutical Sciences Soochow UniversitySuzhou 215127China School of Chemistry and Molecular Engineering East China Normal UniversityShanghai 200062China

Mornaphthoate E(MPE)is a prenylated naphthoic acid methyl ester isolated from the roots of a famous Chinese medicinal plant Morinda officinalis and shows remarkable cytotoxicity against several human tumor cell *** the current project,the first total synthesis of(±)-MPE was achieved in seven steps and 5.6%overall *** the in vitro anti-tumor activity of MPE was first assessed for both enantiomers in two breast cancer cells,with the levoisomer exerting slightly better *** in vivo anti-tumor effect was further verified by applying the racemate in an orthotopic autograft mouse ***,MPE exerted promising anti-metastasis activity both in vitro and in vivo and showed no obvious toxicity on mice at the therapeutic *** investigations demonstrated that MPE acted as a tubulin polymerization stabilizer and disturbed the dynamic equilibrium of microtubules via regulating PI3K/Akt *** conclusion,our work has provided a new chemical template for the future design and development of next-generation tubulin-targeting chemotherapies.

关键词： Mornaphthoate E Tubulin inhibitor Antitumor Anti-metastasis Breast cancer PI3K/Akt

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