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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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Evolution of microstructure and properties of a novel Ni-based superalloy during stress relief annealing

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International Journal of Minerals,Metallurgy and Materials 2024年第8期31卷 1876-1889页

作者： lei Jia Heng Cui Shufeng Yang Shaomin lü Xingfei Xie Jinglong qu Collaborative Innovation Center of Steel Technology University of Science and Technology BeijingBeijing 100083China State Key laboratory of Advanced Metallurgy University of Science and Technology BeijingBeijing 100083China Beijing GAONA Materials&Technology Co. Ltd.Beijing 100081China High-Temperature Materials Institute Central Iron and Steel Research InstituteBeijing 100081China

We discussed the decrease in residual stress,precipitation evolution,and mechanical properties of GH4151 alloy in different annealing temperatures,which were studied by the scanning electron microscope(SEM),high-resolution transmission electron microscopy(HRTEM),and electron backscatter diffraction(EBSD).The findings reveal that annealing processing has a significant impact on diminishing residual *** the annealing temperature rose from 950 to 1150℃,the majority of the residual stresses were relieved from 60.1 MPa down to 10.9 ***,the stress relaxation mechanism transitioned from being mainly controlled by dislocation slip to a combination of dislocation slip and grain boundary ***,the annealing treatment promotes the decomposition of the laves,accompanied by the precipitation ofμ-(Mo_(6)Co_(7))starting at 950℃ and reaching a maximum value at 1050℃.The tensile strength and plasticity of the annealing alloy at 1150℃ reached the maximum(1394 MPa,56.1%)which was 131%,200%fold than those of the as-cast alloy(1060 MPa,26.6%),but the oxidation process in the alloy was accelerated at 1150℃.The enhancement in durability and flexibility is primarily due to the dissolution of the brittle phase,along with the shape and dispersal of theγ′phase.

关键词： GH4151 alloy annealing treatment residual stress precipitation evolution strength mechanical properties

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Design and optimization of a greener sinomenine hydrochloride preparation process considering variations among different batches of the medicinal herb

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Chinese Journal of Chemical Engineering 2024年第7期71卷 77-90页

作者： Dandan Ren Jiale Xie Tianle Chen Haibin qu Xingchu Gong Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China National Key laboratory of Chinese Medicine Modernization Zhejiang UniversityHangzhou 310058China Jinhua Institute of Zhejiang University Jinhua 321016China

The current methods used to industrially produce sinomenine hydrochloride involve several issues,including high solvent toxicity,long process flow,and low atomic utilization efficiency,and the greenness scores of the processes are below 65 *** solve these problems,a new process using anisole as the extractant was *** exhibits high selectivity for sinomenine and can be connected to the subsequent water-washing *** alkalization of the medicinal material,heating extraction,water washing,and acidification crystallization were carried *** process was modeled and *** design space was *** recommended operating ranges for the critical process parameters were 3.0–4.0 h for alkalization time,60.0–80.0℃ for extraction temperature,2.0–3.0(volume ratio)for washing solution amount,and 2.0–2.4 mol·l^(-1) for hydrochloric acid *** new process shows good robustness because different batches of medicinal materials did not greatly impact crystal purity or sinomenine transfer *** sinomenine transfer rate was about 20%higher than that of industrial *** greenness score increased to 90 points since the novel process proposed in this research solves the problems of long process flow,high solvent toxicity,and poor atomic economy,better aligning with the concept of green chemistry.

关键词： Sinomenine hydrochloride Process optimization Anisole

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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry traces the geographical source of Biomphalaria pfeifferi and Bulinus forskali,involved in schistosomiasis transmission

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Infectious Diseases of Poverty 2024年第1期13卷 98-99页

作者： Papa Mouhamadou Gaye ei Hadj Ibrahima Ndiaye Souleymane Doucoure Doudou Sow Mapenda Gaye Ndiaw Goumballa Carole Cassagne Coralie l'Ollivier Oleg Medianikov Cheikh Sokhna Stephane Ranque Aix-Marseille University IRD AP-HM SSA VITROME Marseille France VITROME International IRD-UCAD Campus Dakar Senegal Hospital-University Institut (IHU) Mediterranée Infection Marseille France Departement of Animal Biology Faculty of Sciences and Techniques UCAD Dakar Senegal Department of Parasitology-Mycology UFR Sciences de la Santé Université Gaston Berger Saint-Louis Senegal

Background Freshwater snails of the genera Bulinus spp.,Biomphalaria spp.,and Oncomelania *** the main intermediate hosts of human and animal *** of these snails has long been based on mor-phological and/or genomic criteria,which have their *** limitations include a lack of precision for the morphological tool and cost and time for the DNA-based ***,Matrix-Assisted laser Desorp-tion/lonization Time-Of-Flight(MAlDI-TOF)mass spectrometry,a new tool used which is routinely in clinical microbi-ology,has emerged in the field of malacology for the identification of freshwater *** study aimed to evaluate the ability of MAlDI-TOF MS to identify Biomphalaria pfeifferi and Bulinus forskali snail populations according to their *** This study was conducted on 101 *** and 81 *** snails collected in three distinct geo-graphical areas of Senegal(the North-East,South-East and central part of the country),and supplemented with wild and laboratory *** which had previously been morphologically described were identified by MAlDl-TOF MS[identification log score values(lSV)≥1.7],after an initial blind test using the pre-existing *** DNA-based identification,new reference spectra of ***(n=10)and ***(n=5)from the geographical areas were added to the MAlDI-TOF spectral *** final blind test against this updated database was per-formed to assess identification at the geographic source *** MAlDI-TOF MS correctly identified 92.1%of 101 *** snails and 98.8%of 81 *** *** the final blind test,88%of 166 specimens were correctly identified according to both their species and sampling site,with lSVs ranging from 1.74 to *** geographical source was adequately identified in 90.1%of 91 *** and 85.3%of 75 *** *** Our findings demonstrate that MAlDI-TOF MS can identify and differe

关键词： Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Snail Intermediate host Biomphalaria pfeifferi Bulinus forskali Schistosomiasis Senegal

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Synthesis of NaY zeolite from a submolten depolymerized perlite:Alkalinity effect and crystallization kinetics

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Chinese Journal of Chemical Engineering 2024年第6期70卷 130-138页

作者： Yanli qu Peng Dong li Yang Yuanyuan Yue Haoliang Wang Jingcai Cheng Chao Yang CAS Key laboratory of Green Process and Engineering State Key Laboratory of Petroleum Molecular&Process EngineeringInstitute of Process EngineeringChinese Academy of SciencesBeijing 100190China School of Chemical Engineering University of Chinese Academy of SciencesBeijing 100190China Qingyuan Innovation laboratory Quanzhou 362801China National Engineering Research Center of Chemical Fertilizer Catalyst College of Chemical EngineeringFuzhou UniversityFuzhou 350108China

NaY zeolites are synthesized using submolten salt depolymerized natural perlite mineral as the main silica and alumina sources in a 0.94 l stirred *** of alkalinity ranging from 0.38 to 0.55(n(Na_(2)O)/n(SiO_(2)))on the relative crystallinity,textural properties and crystallization kinetics were *** results show that alkalinity exerts a nonmonotonic influence on the relative crystallinity and textural properties,which exhibit a maximum at the alkalinity of *** nucleation kinetics are studied by fitting the experimental data of relative crystallinity with the Gualtieri *** is shown that the nucleation rate constant increases with increasing alkalinity,while the duration period of nucleation decreases with increasing *** n(Na_(2)O)/n(SiO_(2))ratios ranging from 0.38 to 0.55,the as-synthesized NaY zeolites exhibit narrower crystal size distributions with the increase in *** growth rates determined from the variations of average crystal size with time are 51.09,157.50,46.17 and 24.75 nm·h^(-1),*** is found that the larger average crystal sizes at the alkalinity of 0.38 and 0.43 are attributed to the dominant role of crystal growth over ***,the combined action of prominent crystal growth and the longer duration periods of nucleation at the alkalinity of 0.38 and 0.43 results in broader crystal size *** findings demonstrate that control of the properties of NaY zeolite and the crystallization kinetics can be achieved by conducting the crystallization process in an appropriate range of alkalinity of the reaction mixture.

关键词： NaY zeolite Submolten salt depolymerized perlite Alkalinity Crystallization kinetics

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Synthesis of waterborne polyurethane-humic acid cross-linked biomass porous materials for the adsorption of methylene blue

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Chinese Journal of Chemical Engineering 2024年第3期67卷 27-38页

作者： Shanghong Ma Jianbo qu Haitao Zhang Xiubin Cui Peng Ye Qingfei Hu Mingzhen Chao State Key laboratory of Biobased Material and Green Papermaking Qilu University of TechnologyShandong Academy of SciencesJinan 250353China Faculty of light Industry Qilu University of TechnologyShandong Academy of SciencesJinan 250353China

A series of adsorbent materials(WPU-HAx-y)with a three-dimensional porous structure,green sustainability,and excellent performance were prepared and evaluated for the removal of methylene blue using nontoxic and environmentally friendly waterborne polyurethane as the matrix material and humic acid,a biomass material,as the functional *** newly synthesized adsorbents were characterized by infrared spectroscopy,scanning electron microscopy,specific surface area,and *** effects of contact time(0-8 h),starting concentration(10-100 mg·l^(-1)),pH(3-11),solution temperature(30-60℃),and coexisting ions(Ca2+,Na+,K+,Mg2+)on the performance were ***-first-order,pseudo-second-order,elovich,and intra-particle diffusion models were used to analyze the adsorption kinetics;the langmuir,Freundlich,Temkin,and Dubin-Radushkovich adsorption isotherms were evaluated;and the adsorption behavior of the adsorbent materials was found to be more appropriate for the pseudo-second-order model for chemical pollutant removal than the langmuir model,which depends on monolayer ***-HA2-3 stood out with a maximum adsorption capacity of 813.0081 mg·g^(-1) fitted to the pseudo-second-order and 309.2832 mg·g^(-1) fitted to the langmuir model,showing superior adsorption performance and regenerability.

关键词： Porous media Bioenergy Sustainability Waste water

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Berry-Esseen bounds and Cramér-type moderate deviations for the sample mean and the MlE of the growth rate for a jump-type CIR process

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Acta Mathematica Sinica,English Series 2024年

作者： Fuqing GAO Zhi qu School of Mathematics and Statistics Wuhan University

We study Berry-Esseen bounds and Cramér-type moderate deviations of a jump-type CoxIngersoll-Ross(CIR) process driven by a standard Wiener process and a subordinator. In the subcritical case, we obtain the best Berry-Esseen bound of the sample mean and the MlE of the growth rate if the lévy measure of the subordinator has finite third order moment. Under the Cramér condition,we establish the Cramér-type moderate deviations of the MlE of the growth rate. We first derive a Berry-Esseen bound, a deviation inequality and the Cramér-type moderate deviations for the sample mean of the CIR process by analyzing the asymptotic behaviors of the characteristic function and the moment generating function of the sample mean. Then we analyze a type of additive functional of the jump-type CIR process and use a transformation to study the Berry-Esseen bound and the Cramér-type moderate deviations for the MlE of the growth rate.

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quantitative assessment of the breast cancer marker HER2 using a gold nanoparticle-based lateral flow immunoassay

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Nano Research 2024年第6期17卷 5452-5460页

作者： liya Ye Xinxin Xu Aihua qu liqiang liu Chuanlai Xu Hua Kuang International Joint Research laboratory for Biointerface and Biodetection and School of Food Science and TechnologyJiangnan UniversityWuxi 214122China

Human epidermal growth factor receptor 2(HER2)is an important biomarker for detection and treatment of breast *** this study,we developed monoclonal antibodies against the extracellular domain(ECD)of HER2 and established a rapid and accurate lateral flow immunoassay(lFIA)for use in community medical *** gene sequence of human HER2-ECD was obtained from the National Center for Biotechnology Information(NCBI)to construct the expression ***2-ECD protein expressed in HEK293F cells was used to immunize BAlB/c *** monoclonal antibodies were produced in mouse ascites and isolated by hybridoma cell *** were analyzed for purity by SDS-PAGE(sodium dodecyl sulphate-polyacrylamide gel-electrophoresis)and affinity was assessed by enzyme-linked immunosorbent assay(ElISA)while subtypes were detected using the commercial *** HER2-ECD test strip was prepared based on the sandwich method and evaluated using a portable detection *** affinity of the paired antibodies,4D8 and 8D9,both reached 1×108 l/*** antibodies specifically recognized the HER2-ECD protein in *** limit of detection(lOD)of the gold nanoparticle(AuNP)-based lFIA was 1.7 ng/ml with a detection range of 1.7-400 ng/ml,and the performance of the HER2-ECD strip correlated well with that of a Siemens chemiluminescent immunoassay(ClIA)*** conclusion,the paired antibodies were successfully prepared with high affinity and *** AuNP-based lFIA of HER2-ECD provides a fast and accurate method to detect the concentration of HER2-ECD in serum samples for clinical use in community medical institutions,and could contribute to determining the progress of the disease or the effectiveness of treatment.

关键词： human epidermal growth factor receptor 2 breast cancer monoclonal antibody quantitative lateral flow immunoassay

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Real-time model correction using Kalman filter for Raman-controlled cell culture processes

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Chinese Journal of Chemical Engineering 2024年第6期70卷 251-260页

作者： Xiaoxiao Dong Zhuohong He Xu Yan Dong Gao Jingyu Jiao Yan Sun Haibin Wang Haibin qu Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China Hisun Biopharmaceutical Co.ltd. Hangzhou 311404China

Raman spectroscopy has found extensive use in monitoring and controlling cell culture *** this context,the prediction accuracy of Raman-based models is of paramount ***,models established with data from manually fed-batch cultures often exhibit poor performance in Raman-controlled ***,there is a need for effective methods to rectify these *** objective of this paper is to investigate the efficacy of Kalman filter(KF)algorithm in correcting Raman-based models during cell ***,partial least squares(PlS)models for different components were constructed using data from manually fed-batch cultures,and the predictive performance of these models was ***,various correction methods including the PlS-KF-KF method proposed in this study were employed to refine the PlS ***,a case study involving the auto-control of glucose concentration demonstrated the application of optimal model correction *** results indicated that the original PlS models exhibited differential performance between manually fed-batch cultures and Raman-controlled *** glucose,the root mean square error of prediction(RMSEP)of manually fed-batch culture and Raman-controlled culture was 0.23 and 0.40 g·l^(-1).With the implementation of model correction methods,there was a significant improvement in model performance within Raman-controlled *** RMSEP for glucose from updating-PlS,KF-PlS,and PlS-KF-KF was 0.38,0.36 and 0.17 g·l^(-1),***,the proposed PlS-KF-KF model correction method was found to be more effective and stable,playing a vital role in the automated nutrient feeding of cell cultures.

关键词： Raman spectroscopy Model correction Algorithm Model-predictive control Bioprocess

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Sodium butyrate alleviates fructose-induced non-alcoholic fatty liver disease by remodeling gut microbiota to promoteγ-amino butyric acid production

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Food Science and Human Wellness 2024年第2期13卷 961-971页

作者： qu Chen lei Wu Aijia Zhang Chen Wu liuping Cai Yingping Xiao Yingdong Ni Key laboratory of Animal Physiology and Biochemistry Ministry of Agriculture and Rural AffairsNanjing Agricultural UniversityNanjing 210095China State Key laboratory for Managing Biotic and Chemical Threats to the quality and Safety of Agro-products Institute of Agro-product Safety and NutritionZhejiang Academy of Agricultural SciencesHangzhou 310022China

Sodium butyrate(NaB)can regulate lipid metabolism and inhibit hepatic *** study aimed to investigate whether NaB can alleviate fructose-induced hepat ic steatosis via remodeling the gut microbiota and evaluate the anti-fatty liver *** results showed that NaB and NaB-remodeled gut microbiota significantly alleviated fructose-induced hepatic steatosis and increased plasma uric acid and fructose ***,both NaB and NaB-remodeled gut microbiota increased the abundance of lactobacillus and altered the levels of plasma amino acids(upregulating gamma-amino butyric acid(GABA)and downregulating l-glutamic acid and l-arginine)in fructose-exposed *** correlation analysis showed that GABA levels positively correlated with lactobacillus abundance,and increased GABA levels might promote the reduction of the hepatic triglyceride *** studies confirmed that GABA significantly reduced lipid deposition in mouse hepatocytes induced via fructose pretreatment in *** findings suggested that NaB could ameliorate fructose-induced hepatic steatosis by regulating gut microbiota.

关键词： Butyrate Fructose Gut microbiota Hepatic steatosis

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