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OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data

Horticulture Research 2023年第11期10卷 13-26页

作者： Ben-Ben Miao Wei Dong Yi-Xin gu Zhao-Fang Han Xuan Luo Cai-huan Ke Wei-Wei You State Key Laboratory of Marine Environmental Science College of Ocean and Earth SciencesXiamen UniversityXiamen 361102FujianChina Hospital of Stomatology Guanghua School of StomatologyGuangdong Provincial Key Laboratory of StomatologySun Yat-Sen UniversityGuangzhou 510055GuangdongChina College of Fisheries Guangdong Ocean UniversityZhanjiang 524088GuangdongChina Fujian Institute for Sustainable Oceans Xiamen UniversityXiamen 361102FujianChina

With the advancements in high-throughput sequencing technologies such as Illumina,PacBio,and 10X Genomics platforms,and gas/liquid chromatography-mass spectrometry,large volumes of biological data in multiple formats can now be obtained through multi-omics *** is constantly evolving and seeking breakthroughs to solve multi-omics problems;however,it is challenging for most experimental biologists to analyse data using command-line interfaces,coding,and *** on experience with multi-omics,we have developed OmicsSuite,a desktop suite that comprehensively integrates statistics and multi-omics analysis and *** suite has 175 sub-applications in 12 categories,including Sequence,Statistics,Algorithm,Genomics,Transcriptomics,Enrichment,Proteomics,Metabolomics,Clinical,Microorganism,Single Cell,and Table *** created the user interface with Sequence View,Table View,and intelligent components based on JavaFX and the popular Shiny *** multi-omics analysis functions were developed based on BioJava and 300+packages provided by the R CRAN and Bioconductor communities,and it encompasses over 3000 adjustable parameter *** can directly read multi-omics raw data in FastA,FastQ,Mutation Annotation Format,mzML,Matrix,and HDF5 formats,and the programs emphasize data transfer directions and pipeline analysis *** can produce pre-publication images and tables,allowing users to focus on biological *** offersmulti-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in *** enables researchers to freely explore the molecular information contained in multi-omics big data(Source:https://***/OmicsSuite/,Website:https://***,v1.3.9).

关键词： breakthrough tables seeking

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Superconductivity with two-fold symmetry in topological superconductor SrxBi2Se3

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Science China(Physics,Mechanics & Astronomy) 2017年第3期60卷 74-79页

作者： guan Du YuFeng Li J. Schneeloch R. D. Zhong Genda gu huan Yang Hai Lin Hai-Hu Wen National Laboratory of Solid State Microstructures and Department of Physics Nanjing University Nanjing 210093 China Condensed Matter Physics and Materials Science Department Brookhaven National Laboratory Upton New York 11973 USA Collaborative Innovation Center of Advanced Microstructures Nanjing University Nanjing 210093 China

Topological superconductivity is the quantum condensate of paired electrons with an odd parity of the pairing function. By using a Corbino-shape like electrode configuration, we measure the c-axis resistivity of the recently discovered superconductor SrxBi2Se3 with the magnetic field rotating within the basal planes, and find clear evidence of two-fold superconductivity. The Lane diffraction measurements on these samples show that the maximum gap direction is either parallel or perpendicular to the main crystallographic axis. This observation is consistent with the theoretical prediction and strongly suggests that SrxBi2Se3 is a topological superconductor.

关键词： topological phase pairing symmetries transport properties

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An adsorption study of^99Tc using nanoscale zero-valent iron supported on D001 resin

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Frontiers in Energy 2020年第1期14卷 11-17页

作者： Lingxiao FU Jianhua ZU Linfeng HE Enxi gu huan WANG School of Nuclear Science and Engineering Shanghai Jiao Tong UniversityShanghai200240China Shanghai Institute of Measurement and Testing Technology Shanghai201203China

Nanoscale zero-valent iron(nZVI)supported on D001 resin(D001-nZVI)was synthesized for adsorption of high solubility and mobility radionuclide^***(VII),a chemical substitute for^99Tc,was utilized in batch experiments to investigate the feasibility and adsorption mechanism toward Tc(VII).Factors(pH,resin dose)affecting Re(VII)adsorption were *** high adsorption efficiency of Re(VII)at pH=3 and the solid-liquid ratio of 20 g/L.X-ray diffraction patterns revealed the reduction of ReO^?4 into ReO2 immobilized in *** on the optimum conditions of Re(VII)adsorption,the removal experiments of Tc(VII)were conducted where the adsorption efficiency of Tc(VII)can reach 94%.Column experiments showed that the Thomas model gave a good fit to the adsorption process of Re(VII)and the maximum dynamic adsorption capacity was 0.2910 mg/g.

关键词： technetium nanoscale zero-valent iron(nZVI) D001 resin adsorption

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Unleashing the Power of Bio-based Thermotropic Liquid Crystal Modifiers:Toughening and Reinforcing Petroleum-based Epoxy Resin without Compromising Other Properties

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Chinese Journal of Polymer Science 2024年第8期42卷 1093-1102页

作者： Qing-Yun Lu Hong-Wei gu Jia-Hui Li Qian-Qian Fan Bei-Tao Liu Yan Kou Xi-Gao Jian Zhi-huan Weng State Key Laboratory of Fine Chemicals Frontiers Science Center for Smart MaterialsLiaoning Technology Innovation Center of High Performance Resin MaterialsDepartment of Polymer Science&EngineeringDalian University of TechnologyDalian 116024China Thermochemistry Laboratory Liaoning Province Key Laboratory of Thermochemistry for Energy and MaterialsDalian National Laboratory for Clean EnergyDalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023China

Toughening the petroleum-based epoxy resin blends with bio-based modifiers without compromising their modulus,mechanical strength,and other properties is still a big challenge in view of the *** this study,a bio-based liquid crystal epoxy resin(THMT-E P)with an s-triazine ring structure was utilized to modify a petroleum-based bisphenol A epoxy resin(E51)with 4,4'-diaminodiphenylsulfone(DDS)as a curing agent,and the blended systems were evaluated for their thermal stability,mechanical properties,and flame *** results showed that the impact strength of the blended system initially increased and then decreased with the increase in THMT-EP content,and it reached the a maximum value of 26.5 kJ/m^(2)when the THMT-EP content was 5%,which was 31.2%higher than that of E51/***,the flexural strength,modulus,and glass transition tem perature of the blended system were all simultaneously improved with the addition of *** the same time,the addition of THMT-EP enhanced the flame retardancy of the system by increasing the char yield at 700℃and decreasing the peak heat release rate and total heat release *** work paves the way for a more sustainable improvement in the comprehensive performance of epoxy resin.

关键词： Epoxy resin Toughening Bio-based Thermotropic liquid crystal

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SLC6A14 promotes ulcerative colitis progression by facilitating NLRP3 inflammasome-mediated pyroptosis

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World Journal of Gastroenterology 2024年第3期30卷 252-267页

作者： Qing gu huan Xia Yue-Qiong Song Jun Duan Yun Chen You Zhang He-Ping Chen Li Zhang Department of Elderly Digestive Sichuan Academy of Medical Sciences and Sichuan Provincial People’s HospitalUniversity of Electronic Science and TechnologyChengdu 610072Sichuan ProvinceChina Geriatrics Research Institute Sichuan Provincial People’s HospitalChengdu 610072Sichuan ProvinceChina

BACKGROUND Ulcerative colitis(UC)is an inflammatory condition with frequent relapse and *** suggests the involvement of SLC6A14 in UC pathogenesis,but the central regulator remains *** To explore the role of SLC6A14 in UC-associated *** Quantitative real-time polymerase chain reaction(qRT-PCR),immunoblotting,and immunohistochemical were used to assess SLC6A14 in human UC ***(LPS)was used to induce inflammation in FHC and NCM460 cells and model enteritis,and SLC6A14 levels were *** markers were quantified using enzyme-linked immunosorbent assay,Western blotting,and qRT-PCR,and EdU incubation,CCK-8 assays and flow cytometry were used to examine proliferation and *** models of UC were used for *** SLC6A14 was increased and correlated with NLRP3 in UC ***-induced FHC and NCM460 cells showed increased SLC6A14 *** SLC6A14 increased cell proliferation and suppressed *** SLC6A14 decreased pyroptosis-associated proteins(ASC,IL-1β,IL-18,NLRP3).NLRP3 overexpression counteracted the effects of sh-SLC6A14 on LPS-induced FHC and NCM460 cell ***6A14 improved the mucosa in mice with dextran sulfate sodium-induced *** SLC6A14 promotes UC pyroptosis by regulating NLRP3,suggesting the therapeutic potential of modulating the SLC6A14/NLRP3 axis.

关键词： Ulcerative colitis SLC6A1 NLRP3 Pyroptosis Inflammasome

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Ductular reaction in non-alcoholic fatty liver disease:When Macbeth is perverted

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World Journal of Hepatology 2023年第6期15卷 725-740页

作者： Yang-huan He Jia-Xing Pan Lei-Ming Xu Ting gu Yuan-Wen Chen Department of Gastroenterology and Department of Geriatrics Huadong Hospital Affiliated to Fudan UniversityShanghai 200040China Department of Gastroenterology Xinhua HospitalShanghai Jiaotong University School of MedicineShanghai 200092China Department of Gastroenterology School of MedicineXinhua HospitalShanghai Jiaotong UniversitySchool of MedicineShanghai 200092China Department of Gastroenterology Huadong Hospital Affiliated to Fudan UniversityShanghai 200040China

Non-alcoholic fatty liver disease(NAFLD)or metabolic(dysfunction)-associated fatty liver disease is the leading cause of chronic liver diseases defined as a disease spectrum comprising hepatic steatosis,non-alcoholic steatohepatitis(NASH),liver fibrosis,cirrhosis,and hepatic ***,characterized by hepatocyte injury,steatosis,inflammation,and fibrosis,is associated with NAFLD *** reaction(DR)is a common compensatory reaction associated with liver injury,which involves the hepatic progenitor cells(HPCs),hepatic stellate cells,myofibroblasts,inflammatory cells(such as macrophages),and their secreted ***,several studies have shown that the extent of DR parallels the stage of NASH and *** review summarizes previous research on the correlation between DR and NASH,the potential interplay mechanism driving HPC differentiation,and NASH progression.

关键词： Ductular reaction Non-alcoholic steatohepatitis Hepatic progenitor cells Cell differentiation Inflammatory cells Liver fibrosis

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Mechanical Performances of Carbonitriding Films on Cast Iron by Plasma Electrolytic Carbonitriding

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Chinese Physics Letters 2011年第11期28卷 243-245页

作者： PANG Hua ZHANG gu-Ling WANG Xing-Quan LV guo-Hua CHEN huan YANG Si-Ze Beijing National Laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190 Fujian Key Laboratory for Plasma and Magnetic Resonance Department of AeronauticsSchool of Physics and Mechanical and Electrical EngineeringXiamen UniversityXiamen 361005 College of Science Minzu University of ChinaBeijing 100081

The plasma electrolytic carbonitriding(PEC/N)process is applied to cast iron using an aqueous solution of acetamide and glycerin as the *** properties of the carbonitriding layers on cast iron are *** the PEC/N treatment,the microhardness and wear resistance of cast iron are improved significantly compared to the untreated *** the substrate is processed at 350V for 60 s,the coating presents the highest microhardness and it is about 554.14HK0.02,and the coating with the highest hardness has the best wear resistance.

关键词： nitriding wear coating

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Multiomics analyses unveil the involvement of microRNAs in pear fruit senescence under high-or low-temperature conditions

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Horticulture Research 2020年第1期7卷 153-164页

作者： Chao gu huan-Yu Xu Yu-Hang Zhou Jia-Long Yao Zhi-Hua Xie Yang-Yang Chen Shao-Ling Zhang Centre of Pear Engineering Technology Research State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjing 210095China New Zealand Institute of Plant&Food Research Ltd. Private Bag 92169Auckland 1142New Zealand

Senescence leads to declines in fruit quality and shortening of shelf *** is known that low temperatures(LTs)efficiently delay fruit senescence and that high temperatures(HTs)accelerate ***,the molecular mechanism by which temperature affects senescence is ***,through multiomics analyses of fruits subjected to postharvest HT,LT,and room temperature treatments,a total of 56 metabolic compounds and 700 mRNAs were identified to be associated with fruit senescence under HT or LT *** compounds could be divided into antisenescent(I→III)and prosenescent(IV→VI)*** affected the expression of 202 mRNAs to enhance the biosynthesis of prosenescent compounds of types V and VI and to inhibit the accumulation of antisenescent compounds of types II and *** affected the expression of 530 mRNAs to promote the accumulation of antisenescent compounds of types I and II and to impede the biosynthesis of prosenescent compounds of types IV and ***,16 microRNAs were isolated in response to HT or LT conditions and interacted with the mRNAs associated with fruit senescence under HT or LT *** transformation of pear fruit showed that one of these microRNAs,Novel_188,can mediate fruit senescence by interacting with its target ***,both HT and LT conditions can affect fruit senescence by affecting microRNA–mRNA interactions,but the molecular networks are different in pear fruit.

关键词： involvement senescence conditions

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Jianpi Decoction Combined with Medroxyprogesterone Acetate Alleviates Cancer Cachexia and Prevents Muscle Atrophy by Directly Inhibiting E3 Ubiquitin Ligase

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Chinese Journal of Integrative Medicine 2024年第6期30卷 499-506页

作者： LI Qi KONG Zhao-di WANG huan gu Hong-hui CHEN Zhong Li Shi-guang CHEN Yi-qi CAI Yu YANG Zhen-jiang Department of Oncology and Hematology Shenzhen Traditional Chinese Medicine HospitalShenzhenGuangdong Province518033China College of Pharmacy/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education(MOE)of China Jinan UniversityGuangzhou510632China guangdong Key Lab of Traditional Chinese Medicine Information Technology Jinan UniversityGuangzhou510632China

ObjectiveTo provide comprehensive evidence for the anti-cancer cachexia effect of Jianpi Decoction(JP)and to explore its mechanism of anti-cancer *** mouse model of colon cancer(CT26)-induced cancer cachexia(CC)was used to investigate the anti-CC effect of JP combined with medroxyprogesterone acetate(MPA).Thirty-six mice were equally divided into 6 groups:normal control,CC,MPA(100 mg·kg^(−1)·d^(−1)),MPA+low-dose(20 mg·kg^(−1)·d^(−1))JP(L-JP),MPA+medium-dose(30 mg·kg^(−1)·d^(−1))JP(M-JP),and MPA+high-dose(40 mg·kg^(−1)·d^(−1))JP(H-JP)*** successful modeling,the mice were administered by gavage for 11 *** body weight and tumor volume were measured and recorded every 2 d starting on the 8th day after *** liver,heart,spleen,lung,kidney,tumor and gastrocnemius muscle of mice were collected and *** pathological changes of the tumor was observed,and the cross-sectional area of the gastrocnemius muscle was *** protein expressions of STAT3 and E3 ubiquitinase in the gastrocnemius muscle were measured by Western *** addition,an in vitro C2C12 myotube formation model was established to investigate the role of JP in hindering dexamethasone-induced muscle *** vitro experiments were divided into control,model,and JP serum *** 2-d administration,microscopic photographs were taken and myotube diameters were *** blot was performed to measure the protein expressions of STAT3 and E3 *** combined with MPA restored tumor-induced weight loss(P<0.05,***)and muscle fiber size(P<0.01,***).Mechanistically,JP reduced the expression of atrophy-related proteins MuRF1 and MAFbx in tumor-induced muscle atrophy in vivo(P<0.05,***).In addition,JP reduced the expression of atrophy-related proteins MuRF1 and MAFbx and p-STAT3 phosphorylation(P<0.05 or P<0.01 *** group)in C2C12 myotubes treated with dexamethasone in *** of JP combined with MPA restores t

关键词： cancer cachexia muscle atrophy Jianpi Decoction Chinese medicine E3 ubiquitin ligases

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Improvement for creep strength of a second-generation single crystal superalloy by design of heat treatments

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Rare Metals 2024年第1期43卷 342-350页

作者： Wan-Shun Xia Xin-Bao Zhao Jia-Chen Xu Quan-Zhao Yue Qing-Qing Ding huan-Chang Duan Yue-Feng gu Hong-Bin Bei Ze Zhang Institute of Superalloys Science and Technology School of Materials Science and EngineeringZhejiang UniversityHangzhou 310027China State Key Laboratory of Silicon and Advanced Materials School of Materials Science and EngineeringZhejiang UniversityHangzhou 310027China

Design of heat treatments is related to the key technology for development of nickel-based single crystal superalloys(Ni-SXs). Based on the full understanding of the solidification characteristics, this work applies optimization design of heat treatments for a second-generation Ni-SX. Microstructure evolution and creep properties are compared in the material under conventional/standard(Std.) and optimized(Opt.) treatments. For the Std. sample,strong dendritic segregations determine inconsistent microstructure evolution in the dendritic(D) and interdendritic region(ID), while the latter serves as weak area to have the prior microcrack initiation, damaging overall performance of the alloy. The Opt. treatment applies higher homogenization temperature, leading to overall reduced segregations, while not inducing incipient melting. A lower temperature of first-step ageing is used to lower the size ofγ'particles. These help to form the more uniform microstructure in dendritic and interdendritic region and relieve the inconsistent microstructure evolution. The balanced local strength makes ID no longer as the weak area,thus restricting microcrack initiation. Great improvement of high temperature and low stress property is obtained by this progress, leading to the pronounced increase of creep rupture life under 1100 °C/140 MPa.

关键词： Single crystal superalloy Heat treatment Segregation Solidification Creep property

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