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| 1 | Kiwifruit Genome Database(KGD):a comprehensive resource for kiwifruit genomics显示文摘Kiwifruit(Actinidia spp.)plants produce economically important fruits containing abundant,balanced phytonutrients with extraordinarily high vitamin C contents.Since the release of the first kiwifruit reference genome sequence in 2013,large volumes of genome and transcriptome data have been rapidly accumulated for a handful of kiwifruit species.To efficiently store,analyze,integrate,and disseminate these large-scale datasets to the research community,we constructed the Kiwifruit Genome Database(KGD;http://kiwifruitgenome.org/).The database currently contains all publicly available genome and gene sequences,gene annotations,biochemical pathways,transcriptome profiles derived from public RNA-Seq datasets,and comparative genomic analysis results such as syntenic blocks and homologous gene pairs between different kiwifruit genome assemblies.A set of user-friendly query interfaces,analysis tools and visualization modules have been implemented in KGD to facilitate translational and applied research in kiwifruit,which include JBrowse,a popular genome browser,and the NCBI BLAST sequence search tool.Other notable tools developed within KGD include a genome synteny viewer and tools for differential gene expression analysis as well as gene ontology(GO)term and pathway enrichment analysis. | Junyang Yue Jiacheng Liu Wei Tang Ya Qing Wu Xiaofeng Tang Wei Li Ying Yang Lihuan Wang Shengxiong Huang Congbing Fang Kun Zhao Zhangjun Fei Yongsheng Liu Yi Zheng | 2020 | Horticulture Research2020，7，1： | 6 |
| 2 | Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis显示文摘Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C.However,the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions.Here,we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv.‘Hongyang’,named Hongyang v4.0,which is the first to achieve two de novo haploid-resolved haplotypes,HY4P and HY4A.HY4P and HY4A have a total length of 606.1 and 599.6 Mb,respectively,with almost the entire telomeres and centromeres assembled in each haplotype.In comparison with Hongyang v3.0,the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions,resulting in∼38.6–39.5 Mb extra sequences,which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A,respectively.Furthermore,our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres.Globally,centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer(Ach-CEN153)with different copy numbers among chromosomes.Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids,but also have genetic features for participation in the regulation of cell division.The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement. | Junyang Yue Qinyao Chen Yingzhen Wang Lei Zhang Chen Ye Xu Wang Shuo Cao Yunzhi Lin Wei Huang He Xian Hongyan Qin Yanli Wang Sijia Zhang Ying Wu Songhu Wang Yi Yue Yongsheng Liu | 2023 | Horticulture Research2023，10，2： | 4 |
| 3 | Accessing Alignments of Ontologies via IoT Based on SKOS Data Model显示文摘Many ontologies are provided to representing semantic sensors data.However,heterogeneity exists in different sensors which makes some service operators of Internet of Thing(IoT) difficult(such as such as semantic inferring,non-linear inverted index establishing,service composing) .There is a great deal of research about sensor ontology alignment dealing with the heterogeneity between the different sensor ontologies,but fewer solutions focus on exploiting syntaxes in a sensor ontology and the pattern of accessing alignments.Our solution infers alignments by extending structural subsumption algorithms to analyze syntaxes in a sensor ontology,and then combines the alignments with the SKOS model to construct the integration sensor ontology,which can be accessed via the IoT.The experiments show that the integration senor ontology in the SKOS model can be utilized via the IoT service,and the accuracy of our prototype,in average,is higher than others over the four real ontologies. | Xiulei Liu Xia Hou Junyang Yu Ying Gao Yue Zhang Yingying Zhang | 2017 | China Communications2017，14，6： | 3 |
| 4 | Data-Driven Discovery of Stochastic Differential Equations显示文摘Stochastic differential equations(SDEs)are mathematical models that are widely used to describe complex processes or phenomena perturbed by random noise from different sources.The identification of SDEs governing a system is often a challenge because of the inherent strong stochasticity of data and the complexity of the system’s dynamics.The practical utility of existing parametric approaches for identifying SDEs is usually limited by insufficient data resources.This study presents a novel framework for identifying SDEs by leveraging the sparse Bayesian learning(SBL)technique to search for a parsimonious,yet physically necessary representation from the space of candidate basis functions.More importantly,we use the analytical tractability of SBL to develop an efficient way to formulate the linear regression problem for the discovery of SDEs that requires considerably less time-series data.The effectiveness of the proposed framework is demonstrated using real data on stock and oil prices,bearing variation,and wind speed,as well as simulated data on well-known stochastic dynamical systems,including the generalized Wiener process and Langevin equation.This framework aims to assist specialists in extracting stochastic mathematical models from random phenomena in the natural sciences,economics,and engineering fields for analysis,prediction,and decision making. | Yasen Wang Huazhen Fang Junyang Jin Guijun Ma Xin He Xing Dai Zuogong Yue Cheng Cheng Hai-Tao Zhang Donglin Pu Dongrui Wu Ye Yuan Jorge Gonçalves Jürgen Kurths Han Ding | 2022 | Engineering2022，，10： | 1 |
| 5 | Applying heteroatom co-doped carbon nanotube for manifesting high performance in the electrochemical reduction of aqueous nitrogen oxide by gold nanoparticles显示文摘Electrochemical NO-to-NH_(3) under ambient conditions could be a viable alternative having advantages in terms of energy consumption and exhaust gas recycling of NO,replacing a traditional ammonia synthesis method of the Haber–Bosch process.In synthesizing boron(B-)and nitrogen(N-)co-doped carbon nanotube(CNT)based gold(Au)catalysts,B-dopants elevate the conductivity of carbon nanotube by sp2 hybridization on graphene and implant B–N domains within the graphene layer,and result in facilitating the embedding amount of Au accompanied by high dispersibility with low particle size.Theoretical density functional theory(DFT)calculations elucidate that the electron cloud transmitted from B-dopant to the active site of Au induces the Lewis acidic site,and the O-distal pathway occurs following a spontaneous reaction.Increment of the electron-deficient B-doping area accompanied by N-defects and B–O edges retains the major valence state of Au as Au^(δ+),and suppresses hydrogen evolution reaction(HER)by repulsing the hindrance of H*.This record exhibits the highest faradaic efficiency(FE)of 94.7%,and NH_(3) yield rate of 1877.4μg·h^(-1)·mg_(cat)^(-1),which is the optimal yield over energy consumption in the field of the ambient reduction of aqueous NO. | Jane Chung Haibo Yin Rong Wang Yunlong Wang Junyang Zhang Yue Peng Joung Woo Han Seongyun Ryu Junhua Li | 2024 | Nano Research2024，17，3： | 0 |
| 6 | quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification显示文摘A high-quality genome is the basis for studies on functional,evolutionary,and comparative genomics.The majority of attention has been paid to the solution of complex chromosome structures and highly repetitive sequences,along with the emergence of a new‘telomere-to-telomere(T2T)assembly’era.However,the bioinformatic tools for the automatic construction and/or characterization of T2T genome are limited.Here,we developed a user-friendly web toolkit,quarTeT,which currently includes four modules:AssemblyMapper,GapFiller,TeloExplorer,and CentroMiner.First,AssemblyMapper is designed to assemble phased contigs into the chromosome-level genome by referring to a closely related genome.Then,GapFiller would endeavor to fill all unclosed gaps in a given genome with the aid of additional ultra-long sequences.Finally,TeloExplorer and CentroMiner are applied to identify candidate telomere and centromere as well as their localizations on each chromosome.These four modules can be used alone or in combination with each other for T2T genome assembly and characterization.As a case study,by adopting the entire modular functions of quarTeT,we have achieved the Actinidia chinensis genome assembly that is of a quality comparable to the reported genome Hongyang v4.0,which was assembled with the addition of manual handling.Further evaluation of CentroMiner by searching centromeres in Arabidopsis thaliana and Oryza sativa genomes showed that quarTeT is capable of identifying all the centromeric regions that have been previously detected by experimental methods.Collectively,quarTeT is an efficient toolkit for studies of large-scale T2T genomes and can be accessed at http://www.atcgn.com:8080/quarTeT/home.html without registration. | Yunzhi Lin Chen Ye Xingzhu Li Qinyao Chen Ying Wu Feng Zhang Rui Pan Sijia Zhang Shuxia Chen Xu Wang Shuo Cao Yingzhen Wang Yi Yue Yongsheng Liu Junyang Yue | 2023 | Horticulture Research2023，10，8： | 0 |
| 7 | SSR2Marker: an integrated pipeline for identification of SSR markers within any two given genome-scale sequences显示文摘Introduction Simple sequence repeats(SSRs),also known as microsatellites,are typically comprised of 1–6 nucleotide units repeated in tandem patterns(Ellegren 2004).Due to their high level of polymorphism,SSRs have become one of the most commonly used molecular markers for species identification,diversity assessment,linkage mapping,molecular breeding and QTL analysis(Vieira et al.2016).Therefore,exploration and exploitation of SSR markers have attracted intense interests in plant breeding programs for the genotype and phenotype linkage analysis.However,traditionally experimental screening of SSR markers is extremely labor-intensive and timeconsuming.With tremendously increasing volumes of high-throughput sequencing data,many bioinformatics tools have been proposed for automated SSR discovery and/or marker screening,but they have certain limitations in target sequence extraction,large-size data handling and/or overall performance(Supplementary Table 1). | Junyang Yue Yongsheng Liu | 2022 | Molecular Horticulture2022，2，1： | 0 |
| 8 | Bimetallic AgNi nanoparticles anchored onto MOF-derived nitrogen-doped carbon nanostrips for efficient hydrogen evolution显示文摘Hydrogen energy has long been recognized as a clean alternative to conventional fossil fuels,which can be applied in a wide range of transportation and power generation applications.The rational design and engineering of high-performance and robust catalysts for hydrogen evolution reaction(HER)shows not a great significance but a challenge for efficient electrochemical water splitting.Herein,a new type of Nibased Ni-ABDC precursor has been obtained,which leads to the formation of N-doped porous carbon nanomaterials uniformly coated with wellproportioned bimetallic AgNi alloys via a stepwise strategy.To their credit,all samples of AgNi/NC-X are structurally calcined from the pristine AgNi-ABDC-X by tuning the different concentration of AgNO3,which means all of them maintain the vermicelli-like morphology compared with Ni-ABDC.The series of AgNi/NC-X materials can be regarded as effective electrocatalysts for HER both in acidic and alkaline media,but an acid-leaching phenomenon is observed.Among them,the as-prepared AgNi/NC-2 exhibits a low overpotential of 103 mV at the current density of 10 mA cm^(-2)and decent durability with a high retention rate of 90.9%after 10 h in 1.0 mol L^(-1)KOH electrolyte.The compelling HER properties of AgNi/NC-2 can be attributed to the synergistic effect between the hierarchical carbon materials,partial N-doping and abundant AgNi alloys.Meanwhile,this study provides a practicable method for the development of efficient HER electrocatalysts for energy applications,which can be conveniently prepared through the reasonable introduction of active components in the crystalline inorganic-organic precursors.©2021 Institute of Process Engineering,Chinese Academy of Sciences.Publishing services by Elsevier B.V.on behalf of KeAi Communications Co.,Ltd.This is an open access article under the CC BY-NC-ND license(http://creativecommons.org/licenses/by-nc-nd/4.0/). | Dandan Chen Cheng Han Qiuhong Sun Junyang Ding Qi Huang Ting-Ting Li Yue Hu Jinjie Qian Shaoming Huang | 2023 | Green Energy & Environment2023，8，1： | 0 |
| 9 | Heterobifunctional PEG-grafted black phosphorus quantum dots: “Three-in-One”nano-platforms for mitochondria-targeted photothermal cancer therapy显示文摘Black phosphorus(BP)nano-materials,especially BP quantum dots(BPQDs),performs outstanding photothermal antitumor effects,excellent biocompatibility and biodegradability.However,there are several challenges to overcome before offering real benefits,such as poor stability,poor dispersibility as well as difficulty in tailoring other functions.Here,a“three-in-one”mitochondria-targeted BP nano-platform,called as BPQD-PEG-TPP,was designed.In this nano-platform,BPQDs were covalently grafted with a heterobifunctional PEG,in which one end was an aryl diazo group capable of reacting with BPQDs to form a covalent bond and the other end was a mitochondria-targeted triphenylphosphine(TPP)group.In addition to its excellent near-infrared photothermal properties,BPQD-PEG-TPP had much enhanced stability and dispersibility under physiological conditions,efficient mitochondria targeting and promoted ROS production through a photothermal effect.Both in vitro and in vivo experiments demonstrated that BPQD-PEG-TPP performed much superior photothermal cytotoxicity than BPQDs and BPQD-PEG as the mitochondria targeted PTT.Thus this“three-in-one”nanoplatform fabricated through polymer grafting,with excellent stability,dispersibility and negligible side effects,might be a promising strategy for mitochondria-targeted photothermal cancer therapy. | Junyang Qi Yue Xiong Ke Cheng Qi Huang Jingxiu Cao Fumei He Lin Mei Gan Liu Wenbin Deng | 2021 | Asian Journal of Pharmaceutical Sciences2021，16，2： | 0 |
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