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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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Improved ecological development model for lower Yellow River floodplain,China

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Water Science and Engineering 2020年第4期13卷 275-285页

作者： Jin-liang zhang yi-zi Shang Ji-xiang Liu Jian Fu Meng Cui Yellow River Engineering Consulting Co. Ltd.Zhengzhou 450003China State Key Laboratory of Simulation and Regulation of Water Cycle in River Basins China Institute of Water Resources and Hydropower ResearchBeijing 100038China

In this study,a model for the development of the wide floodplain in the lower Yellow River Basin,in China was *** model includes flood control schemes using grading criteria,enables sediment deposition in partitioned zones,and allows free exchange between channel runoff and *** wide floodplain located between the main channel and levees is divided into three typical regions:the tender,low,and high *** ecological models should be applied when these floodplains are *** paper describes the associated research ideas and methodology,and clarifies several key issues,including sediment prediction and regulation,land planning,land use,and a multi-dimensional framework of safeguard measures for industries on the lower Yellow River floodplain.A refined ecological development model is proposed for the lower Yellow River floodplain,and future work on ecological and sustainable development of the lower floodplain is *** establish a comprehensive system integrating runoff and sediment resource regulation in the Yellow River Basin,future work should focus on runoff and sediment exchange mechanisms in the wandering lower ***,it is necessary to improve theories on floodplain planning and ecological construction,and these theories should be integrated with the research findings on land development across the lower Yellow River floodplain.©2020 Hohai *** and hosting by Elsevier *** is an open access article under the CC BY-NC-ND license(http://***/licenses/by-nc-nd/4.0/).

关键词： Ecological development Lower Yellow River Floodplain Sediment Eco-friendly construction model

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Hybrid perovskite shows temperature-dependent photoluminescence and dielectric response triggered by halogen substitution

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Chinese Journal of Structural Chemistry 2024年第6期43卷 28-33页

作者： Xiao-Tong Sun Hao-Fei Ni yi zhang Da-Wei Fu Ordered Matter Science Research Center Jiangsu Key Laboratory for Science and Applications of Molecular FerroelectricsSoutheast UniversityNanjing211189People's Republic of China Institute for Science and Applications of Molecular Ferroelectrics Key Laboratory of the Ministry of Education for Advanced Catalysis MaterialsZhejiang Normal UniversityJinhua321004People's Republic of China

Materials exhibiting dielectric switching response and photoluminescence(PL)are promising for sensors and information *** previous research,we synthesized a series of materials with red or green PL and dielectric switching capabilities by incorporating luminescent metal halides into organic ammonium ***,effective modification to synthesize organic-inorganic hybrid materials with dielectric switching response and orange PL continues to be a challenge in the respective *** PL materials are valuable for switching and sensors,and most orange light sources are derived from rare earth elements,making them harder to *** have successfully synthesized two organic-inorganic hybrid materials([CMPD]PbBr_(3)(1)and[BMPD]PbBr_(3)(2),CMPD=N-ClCH_(2)-N-methylpiperidine,BMPD=N-BrCH_(2)-N-methylpiperidine)that exhibit both orange PL and dielectric switching *** Cl in compound 1 is substituted by Br in compound 2,the phase transition temperature of the compound is elevated by 45 *** compounds exhibit captivating orange light emission when exposed to ultraviolet *** research provides insights into exploring multifunctional materials with orange PL and dielectric switching response and provides proof for halogen substitution strategies to design materials with higher phase transition temperatures.

关键词： Dielectric switching Photoluminescence Orange

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Different defect morphologies in polyethylene crystal induced by surface physicochemical properties

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Chinese Chemical Letters 2020年第6期31卷 1640-1643页

作者： Yaqi Hou yi Ye Zhongjie Du Chen zhang Jianguo Mi Xu Hou State Key Laboratory of Organic-Inorganic Composites Beijing University of Chemical TechnologyBeijing 100029China Research Institute for Soft Matter and Biomimetics College of Physical Science and TechnologyXiamen UniversityXiamen 361005China State Key Laboratory of Physical Chemistry of Solid Surfaces College of Chemistry and Chemical EngineeringXiamen UniversityXiamen 361005China College of Materials Science and Engineering Beijing University of Chemical TechnologyBeijing 100029China

The physicochemical properties of surfaces have a great effect on the micro-morphologies of the crystal structures which are in contact with *** the interaction mechanism between the internal driving forces of the crystal and external inducing forces of the surfaces is the prerequisite of controlling and obtaining the desirable *** this work,the dynamic density functional theory was applied to construct the free energy functional expression of polyethylene(PE)lattice,and the micro-dynamic evolution processes of PE lattice morphology near the surfaces with different properties were observed to reveal the interaction mechanism at atomic *** results showed that the physical and chemical properties of the external surfaces synergistically affect the morphologies in both the defect shapes and the distribution of the defect *** the absence of the contact surfaces,driven by the oriented interactions among different CH2 groups,PE lattices gradually grow and form a defect-free ***,the presence of contact surfaces leads to lattice defects in the interfacial regions,and PE lattice shows different self-healing abilities around different surfaces.

关键词： Physicochemical properties External surfaces Defect morphologies Polyethylene crystal Dynamic density functional theory Atomic scale

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Stationarity in the variability of arid precipitation:A case study of aridCentral Asia

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Advances in Climate Change Research 2021年第2期12卷 172-186页

作者： YAO Jun-Qiang CHEN Jing zhang Tong-Wen DILINUER Tuoliewubieke MAO Wei-yi Institute of Desert Meteorology China Meteorological AdministrationUrumqi830002China

Precipitation is particularly scarce in arid Central Asia(CA),and is expected to be severely impacted by future warming,and the assessmentof the stationarity of precipitation variability is important for managing surface water resources in this *** this study,we investigated thestatistics of stationarity in the totals and extremes of precipitation in CA based on the longest observational records(1881e2006),tree-ringreconstructed records(1756e2012 and 1760e2015),and the Coupled Model Intercomparison Project 5(CMIP5)simulations,applying theautocorrelation function and testing criteria established based on the statistical definitions of *** analyzed the longest daily pre-cipitation record(Tashkent station,1881e2006)and found that the autocorrelation coefficient of the precipitation totals(PRCPTOT)and annualmaximum 1-day precipitation amount(Rx1day)were statistically insignificant for all lags,implying stationary ***,nearly allthe Global Historical Climatology Network-Daily Database(GHCN-D)observatory sites(1925e2005)indicated likely stationary *** records were also indistinguishable from a random *** the CMIP5 models,the simulated and projected PRCPTOT closelyapproximated a purely random process;however,the projected Rx1day maintained non-stationary means in most of the models under therepresentative concentration pathway(RCPs),implying that extreme events would increase in the *** mean precipitation changes(DP)can be expressed as an exponential function depending on the length of the successive mean periods(m)and variance(s2).TheDPof the nextdecade is projected to be within±14.8%of the previous decades mean annual PRCPTOT over *** higher the RCPs,the higher theDP *** results show that the detection and prediction of precipitation change will be challenging in arid CA.

关键词： Stationarity Precipitation Extreme precipitation Variance Central Asia

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Effective fraction from Simiao Wan prevents hepatic insulin resistant by inhibition of lipolysis via AMPK activation

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Chinese Journal of Natural Medicines 2022年第3期20卷 161-176页

作者： JIANG Qi-xin CHEN yi-Meng MA Jing-Jie WANG Yu-Ping LI Ping WEN Xiao-Dong YANG Jie State Key Laboratory of Natural Medicines China Pharmaceutical UniversityNanjing 210009China

Simiao Wan(SMW)is a traditional Chinese formula,including Atractylodis Rhizoma,Achyranthis Bidentatae Radix,Phellodendri Chinensis Cortex and Coicis Semen at the ratio of 1:1:2:*** can be used to the treatment of ***,its bioactive compounds and underlying mechanism are *** study was designed to screen the antilipolytic fraction from SMW and investigate its therapeutic mechanisms on hepatic insulin *** fractions of SMW were prepared by membrane separation combined with macroporous resin and their antilipolytic activity was screened in fasted *** effects of 60%ethanol elution(ESMW)on lipolysis were investigated in 3T3-L1 adipocytes stimulated by palmitic acid(PA)and high fat diet(HFD)-fed *** our study,ESMW was the bioactive fraction responsible for the antilipolytic activity of SMW and 13 compounds were characterized from ESMW by UHPLC-QTOF-MS/*** suppressed protein kinase A(PKA)-hormone-sensitive lipase(HSL)related lipolysis and increased AMP-activated protein kinase(AMPK)phosphorylation in PA challenged 3T3-L1 *** knockdown abolished the inhibitory effects of ESMW on IL-6 and HSL pSer-660,revealing that the antilipolytic and anti-inflammatory activities of ESMW are AMPK ***,ESMW ameliorated insulin resistance and suppressed lipolysis in HFD-fed *** inhibited diacylglycerol accumulation in the liver and inhibited hepatic *** medium collected from ESMW-treated 3T3-L1 cells ameliorated insulin action on hepatic gluconeogenesis in liver cells,demonstrating that the antilipolytic activity contributed to ESMW beneficial effects on hepatic glucose *** conclusion,ESMW,as the antilipolytic fraction of SMW,inhibited PKA-HSL related lipolysis by activating AMPK,inhibiting diacylglycerol(DAG)accumulation in the liver and thereby improving insulin resistance and hepatic gluconeogenesis.

关键词： Simiao Wan Insulin resistance Lipolysis AMPK

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Detection of maize tassels for UAV remote sensing image with an improved YOLOX Model

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Journal of Integrative Agriculture 2023年第6期22卷 1671-1683页

作者： SONG Chao-yu zhang Fan LI Jian-sheng XIE Jin-yi YANG Chen ZHOU Hang zhang Jun-xiong College of Engineering China Agricultural UniversityBeijing 100083P.R.China College of Agronomy and Biotechnology China Agricultural UniversityBeijing 100083P.R.China

Maize tassel detection is essential for future agronomic management in maize planting and breeding,with application in yield estimation,growth monitoring,intelligent picking,and disease ***,detecting maize tassels in the field poses prominent challenges as they are often obscured by widespread occlusions and differ in size and morphological color at different growth *** study proposes the SEYOLOX-tiny Model that more accurately and robustly detects maize tassels in the ***,the data acquisition method ensures the balance between the image quality and image acquisition efficiency and obtains maize tassel images from different periods to enrich the dataset by unmanned aerial vehicle(UAV).Moreover,the robust detection network extends YOLOX by embedding an attention mechanism to realize the extraction of critical features and suppressing the noise caused by adverse factors(e.g.,occlusions and overlaps),which could be more suitable and robust for operation in complex natural *** results verify the research hypothesis and show a mean average precision(mAP_(@0.5)) of 95.0%.The mAP_(@0.5),mAP_(@0.5-0.95),mAP_(@0.5-0.95(area=small)),and mAP_(@0.5-0.95(area=medium)) average values increased by 1.5,1.8,5.3,and 1.7%,respectively,compared to the original *** proposed method can effectively meet the precision and robustness requirements of the vision system in maize tassel detection.

关键词： maize tassel detection remote sensing deep learning attention mechanism

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Genesis of Makeng-type Fe-polymetallic deposits in SE China:New constraints by geochronological and isotopic data from the Dapai–Makeng metallogenic system

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Geoscience Frontiers 2023年第5期14卷 189-212页

作者： Absai Vatuva Xiaolong He xinming zhang Da zhang Haibin Feng Yuan Yuan Sen Wang Jinjun yi Yongjun Di China University of Geosciences(Beijing) Beijing 100083China University of Namibia Windhoek Private Bag 13301Namibia Xiangtan University Xiangtan 411105China

The southwestern Fujian depression belt(SFDB)is an economically important Mesozoic Fe metallogenic belt in South China and is renowned for its Makeng-type Fe deposits,in which stratified skarn Fe orebodies generally occur in or near the contact zone between late Paleozoic carbonate sequences and Mesozoic ***,the genesis and geodynamic setting of these deposits remain unclear because the characteristics of the widely distributed Pb–Zn–Cu and Mo orebodies in these deposits and the temporal,spatial,and genetic relationships between magmatism and mineralization are poorly *** Dapai Fe polymetallic deposit in the SFDB is a typical example of Makeng-type Fe deposits but also has regional significance,whereby the stratified skarn Fe orebodies have overprinted the stratabound Pb–Zn–Cu mineralization followed by final fissure-filling by vein-disseminated Mo mineralization.A detailed geological investigation suggests that episodic magmatic–hydrothermal events were involved in the formation process of the Dapai Fe polymetallic *** and sphalerite from the Pb–Zn–Cu orebodies yield an Rb–Sr isochron age of 175.5±3.3 Ma,which is regarded as the timing of Pb–Zn–Cu *** grains from Fe-mineralized granodiorite porphyry and Mo-mineralized monzogranite yield weighted-mean 206Pb/238U ages of 146.3±0.9 Ma and 131.7±0.4 Ma,interpreted as the timings of Fe and Mo mineralization,*** zircons from granodiorite also yield a 206Pb/238U model age cluster of184 Ma,which coincides reasonably with the timing of Pb–Zn–Cu mineralization and implies the existence of an unidentified ore-related intrusion in the Dapai *** further zircons from the porphyritic granodiorite yield an age cluster of-150 Ma,consistent with the timing of Fe ***,pyrite,and sphalerite from the Dapai and Makeng deposits have similar S–Pb isotopic compositions and suggest a magmatic *** our results with published isotopic data fo

关键词： Southwestern Fujian Depression Belt Makeng-type Fe polymetallic deposit Sulfide Rb-Sr dating Zircon U-Pb dating S-Pb-Fe isotopes Geodynamic setting

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Freestanding carbon fiber-confined yolk-shelled silicon-based anode for promoted lithium storage applications

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Rare Metals 2023年第11期42卷 3718-3728页

作者： Dong-Chen Jia Yuan-Yong Feng Chuan-Long zhang Jian-Jiang Li Bin-Wei zhang Yu-Hai Dou Jagadish Chandra Roy Xiao-yi Zhu Lei zhang School of Environmental Science and Engineering Qingdao UniversityQingdao266071China Department of Oral and Maxillofacial Surgery The Affiliated Hospital of Qingdao UniversityQingdao266071China Centre for Catalysis and Clean Energy Gold Coast CampusGriffith UniversitySouthportQLD4222Australia Center of Advanced Energy Technology and Electrochemistry Institute of Advanced Interdisciplinary StudiesSchool of Chemistry and Chemical EngineeringChongqing UniversityChongqing400044China Institute of Energy Materials Science University of Shanghai for Science and TechnologyShanghai200093China

A flexible carbon fiber-confined yolk-shelled silicon-based composite is reported as an anode material for lithium storage *** nanoparticles(Si NPs)are confined by the N-doped hollow carbon cages(SiNHC)and these uniform dispersed yolk-shell-structured Si-NHC units were encapsulated by the carbon fibers within an interconnected three-dimensional(3D)framework(Si-NHC@CNFs).For the encapsulated yolkshelled Si-NHC,the void space between the inner Si NPs and outer NHC can accommodate the structural changes of Si NPs during charging/discharging processes,leading to effectively improved structural stability and cycling *** importantly,all the Si-NHC units were bridged together through a conductive CNFs"highway"to enhance the overall conductivity and tap density *** observed,Si-NHC@CNFs exhibited an initial discharge capacity of 1364.1 mAh·g^(-1)at 1000 mA·g^(-1)and678.9 mAh·g^(-1)at 2000 mA·g^(-1).Furthermore,the reversible capacity was well maintained at 752.2 mAh·g^(-1)at500 mA·g^(-1)after 6000 ultra-long cycles.

关键词： Silicon ZIF-8 Carbon fibers Anode Lithium-ion battery(LIB)

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Scheme of Weather-Based Indemnity Indices for Insuring Against Freeze Damage to Citrus Orchards in Zhejiang,China

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Agricultural Sciences in China 2009年第11期8卷 1321-1331页

作者： LOU Wei-ping QIU xin-fa WU Li-hong NI Hu-ping TANG Qi-yi MAO Yu-ding Department of Atmospheric Science Nanjing University oflnformation Science ＆ Technology Nanjing 210044 P..R.China xinchang Weather Bureau Xinchang 312500 P.R.China Zhejiang Provincial Climate Center Hangzhou 310017 P.R. China Division of Comprehensive Reform Development and Reform Commission of Zhejiang Province Hangzhou 310025 P.R. China College of Agriculture and Biotechnology Zhejiang University Hangzhou 310029 P.R.China

We design a weather-based indemnity index for the insurance against freeze damage to citrus orchards so as to provide technological support for the development of policy-based agriculture. The indices are prepared by separating a relative meteorological yield from the yield that is dependent on tree age, high-yield and low-yield years, and environmental factors, and then using a risk assessment scheme to determine the percentage yield reduction due to the meteorological hazard. We thus develop a set of indices associated with cold temperature damage with which to construct more severe weather indices in conjunction with the yield percentage decrease. We then combine the insured regional citrus yield index with the insured meteorological counterpart to obtain a weather-based indemnity index for the varying degree of freeze damage to crops. When the freeze damage index （FDI） is greater than -7.0℃ for the coastal belt of Zhejiang Province, China, or greater than -9.0℃ for other regions of Zhejiang, weather-based indemnity index （WBII） is zero, meaning there is no compensation; when the FDI is from -7.0 to -7.9℃ for the coastal belt or from -9.0 to -9.9℃ for other regions, the WBII is 1 with 50% compensation; when the FDI is from -8.0 to -8.9℃ for the coastal belt or from -10.0 to -10.9℃ for other regions, the WBII is 2 with 70% compensation; and when the FDI is less than -9.0℃ for the coastal belt or less than -11.0℃ for other regions, the WBII is 3 with 90% compensation. The weather indemnity indices of insured orchards are developed in the interest of owners, thereby eliminating adverse selection and moral hazard issues and providing timely recompense from the insurer, and resolving the problem of high indemnity cost in agricultural insurance.

关键词： citrus orchard freeze damage agricultural insurance weather-based indemnity index

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