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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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Embryonic and larval development of the invasive biofouler Mytilopsis sallei(Récluz,1849)(Bivalvia:Dreissenidae)

Embryonic and larval development of the invasive biofouler M...

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福建省海洋学会2016年学术年会

作者： Jian He Jian Fei Qi Dan Qing Feng cai huan ke College of Ocean & Earth Sciences Xiamen University Fisheries Research Institute of Fujian

The marine dreissenid bivalve Mytilopsis sallei is a fouling organism that has invaded habitats outside its original *** its early development will be useful for early detection in the environment,for species identification in ballast water and for development of control strategies targeted at early life stages,which will help us better manage this important *** processes of embryogenesis,shell formation and larval development of *** are described here for the first time by using light and scanning electron *** oocytes are 64 μm in *** eggs were incubated at 27±1 ℃.The trochophore,with an apical tuft and a prototroch,developed by 6.0±2.3 h postfertilization(hpf).At 16.5±4.2 hpf,D-shaped veligers with shell length(SL,mean±SD)of 87.3±8.2 μm appeared,each possessing a velum and a calcified *** 2-3 days postfertilization(dpf),the D-shaped veligers developed into umbonate larvae(SL=111.9±10.7μm),the last obligate free-swimming veliger ***(SL=232.8±37.1μm)observed at 6-8 dpf could either swim using their velum or crawl with their *** settled by secreting byssal threads and metamorphosed to plantigrades(SL=298.7±45.2 μm)8-10 *** is noteworthy that the larvae of this invasive bivalve are capable of settlement within 10 *** is the first detailed study of early shell formation of a species of the family *** field invagination appeared during gastrulation,secreting shell material by expanding over both sides in a saddle-shape during the trochophore stage.

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Low barnacle fouling on leaves of the mangrove plant Sonneratia apetala and possible anti-barnacle defense strategies

Low barnacle fouling on leaves of the mangrove plant Sonnera...

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福建省海洋学会2016年学术年会

作者： Dan-qing Feng Wei Wang Xiang Wang Yan Qiu cai-huan ke College of Ocean & Earth Sciences Xiamen University Medical College Xiamen University

A field survey of barnacle fouling on leaves of five co-occurring mangrove plants(Kandelia candel,Bruguiera gymnorrhiza,Rhizophora stylosa,Sonneratia apetala,and Avicennia marina) was conducted in Tongan Bay,southeastern *** leaves of *** were found to be less frequently and less abundantly fouled by barnacles relative to the other mangrove species,implying that *** may possess anti-barnacle *** surface wettability and flexibility of leaves for the five investigated mangrove species were *** the lower surface of *** leaf,the leaves of all these species exhibited low surface wettability,with contact angles of 82° to 94°.The leaf flexibility of *** was similar to that of ***,and both were much greater than those of the other three mangrove *** of all these five mangrove species were also subjected to chemical *** extracts of ***,***,*** and *** showed anti-settlement activities against the barnacle Balanus albicostatus,with EC values respectively of 0.85,10.13,37.03,and 50.67 μg/*** antifouling compound,identified as oleanolic acid,was isolated from the two most active extracts(the *** extract and the *** extract) via bioassay-guided fractionation.A potential multiple defense strategy of *** against barnacle fouling,including low surface wettability,anti-barnacle settlement metabolite of oleanolic acid,and post-settlement detachment of barnacles from its flexible leaves,is proposed in this study.

关键词： Mangrove Barnacle fouling Antifouling defense Sonneratia apetala Surface wettability Oleanolic acid

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Insufficient MIRO1 contributes to declined oocyte quality during reproductive aging

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Science China Life Sciences 2025年

作者： Zhen-Nan Pan Hao-Lin Zhang Kun-huan Zhang Jia-Qian Ju Jing-cai Liu Shao-Chen Sun College of Animal Science and Technology Nanjing Agricultural University Reproductive Medicine Centre The Affiliated Yantai Yuhuangding Hospital of Qingdao University

Mitochondrial Rho-GTPase 1 (MIRO1) is an outer mitochondrial membrane protein which regulates mitochondrial transport and mitophagy in mitosis. In present study, we reported the crucial roles of MIRO1 in mammalian oocyte meiosis and its potential relationship with aging. We found that MIRO1 expressed in mouse and porcine oocytes, and its expression decreased in aged mice. MIRO1 deficiency caused the failure of meiotic resumption and polar body extrusion in both mouse and porcine oocytes, which could be rescued by exogenous MIRO1supplementation. Mass spectrometry data indicated that MIRO1 associated with several cytoskeleton and cell cycle-related proteins, and MIRO1 regulated motor protein Dynein for microtubule-organizing centers (MTOCs) dynamics at germinal vesicle (GV) stage, which determined meiotic resumption. Furthermore, we found that MIRO1 regulated Aurora A and kinesin family member 11 (KIF11) for meiotic spindle assembly in oocytes. Besides, MIRO1 associated with several mitochondria-related proteins dynamic-related protein 1 (DRP1),Parkin and lysosomal-associated membrane protein 2 (LAMP2) for mitochondrial dynamics and mitophagy during oocyte meiosis. Taken together, our results suggested that MIRO1 played pivotal roles in meiotic resumption, spindle assembly and mitochondrial function in mouse and porcine oocytes, and its insufficiency might contribute to the oocyte maturation defects during aging.

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Facile intercalation of alkali ions in WO_(3)for modulated electronic and optical properties:Implications for artificial synapses and chromogenic application

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Science China(Physics,Mechanics & Astronomy) 2024年第2期67卷 149-160页

作者： Changmeng huan Zihan Lu Silin Tang Yongqing cai Qingqing ke School of Microelectronics Science and Technology Sun Yat-sen UniversityZhuhai 519082China Guangdong Provincial key Laboratory of Optoelectronic Information Processing Chips and Systems Sun Yat-sen UniversityZhuhai 519082China Institute of Applied Physics and Materials Engineering University of MacaoTaipaMacao 999078China

Tungsten oxides(WO_(3))are widely recognized as multifunctional systems owing to the existence of rich *** diverse phases exhibit distinct octahedra-tilting patterns,generating substantial tunnels that are ideally suited for ***,a quantitative comprehension regarding the impact of distinct phases on the kinetics of intercalated conducting ions remains ***,we employ first-principles calculations to explore the spatial and orientational correlations of ion transport inγ-and h-WO_(3),shedding light on the relationship between diffusion barriers and the size of the conducting *** findings reveal that different types and concentrations of alkali-metals induce distinct and continuous lattice distortions in WO_(3)***,γ-WO_(3)is more appropriate to accommodate Li+ions,exhibiting a diffusion barrier and coefficient of 0.25 eV and 9.31×10^(-8)cm^(2)s^(-1),***,h-WO_(3)features unidirectional and sizeable tunnels that facilitate the transport of K+ions with an even lower barrier and a high coefficient of 0.11 e V and 2.12×10^(-5)cm^(2)s^(-1),***,the introduction of alkali-metal into WO_(3)tunnels tends to introduce n-type conductivity by contributing s-electrons to the unoccupied W 5d states,resulting in enhanced conductivity and tunable electronic *** alkali metals in WO_(3)tunnels are prone to charge transfer,forming small polaronic states and modulating the light absorption in the visible and nearinfrared *** tunable electronic and optical properties,combined with the high diffusion coefficient,underscore the potential of WO_(3)in applications such as artificial synapses and chromogenic devices.

关键词： WO_(3)polymorphs ion insertion kinetic activity tunable electronic and optical properties iontronics

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Direct Approach to Construct the Periodic Wave Solutions for Two Nonlinear Evolution Equations

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Communications in Theoretical Physics 2009年第9期52卷 473-478页

作者： cai ke-Jie TIAN Bo ZHANG huan MENG Xiang-Hua School of Science P.O. Box 122 Beijing University of Posts and Telecommunications Beijing 100876 China State key Laboratory of Software Development Environment Beijing University of Aeronautics and Astronautics Beijing 100191 China key Laboratory of Information Photonics and Optical Communications Ministry of Education Beijing University of Posts and Telecommunications Beijing 100876 China

With symbolic computation, the Hirota method and Riemann theta function are employed to directly construct the periodic wave solutions for the Hirota-Satsuma equation for shallow water waves and Boiti-Leon-Manna- Pempinelli equation. Then, the corresponding figures of the periodic wave solutions are given. Fhrthermore, it is shown that the known soliton solutions can be reduced from the periodic wave solutions.

关键词： periodic wave solutions Hirota-Satsuma equation for shallow water waves Boiti-Leon-Manna-Pempinelli equation Hirota method Riemann theta function

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One-step Eco-friendly Fabrication of Antibacterial Polyester Via On-line Amination Reaction by Melt Coextrusion

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Journal of Wuhan University of Technology(Materials Science) 2023年第5期38卷 1205-1212页

作者： ZHANG huan ZHAO Qinghua ZHONG Yaping cai Ruiyan LIU ke WANG Dong LU Zhentan key Laboratory of Textile Fiber and Products Wuhan Textile UniversityMinistry of EducationHubei International Scientific and Technological Cooperation Base of Intelligent Textile Materials&ApplicationSchool of Materials Science and EngineeringWuhan Textile UniversityWuhan 430200China Guangdong Engineering Technology Research Center of Functional Fibers for Clothing Guangdong BobaolonCo.Ltd.Puning515300China

The work is dedicated to develop a one-step eco-friendly method to prepare antibacterial polyethylene terephthalate(PET).We report a one-step eco-friendly method to manufacture antibacterial PET via on-line amination reaction by melt *** evenly mixing of poly(hexamethylene guanidine)(PHMG)and PET in the melt coextrusion procedure,the amination reaction also occurred between PHMG and PET under high temperature(230-270℃).The antibacterial ability of composite PET showed obvious PHMG concentration dependence,and antibacterial activity reached more than 99%when PHMG content was 2.5 wt%.Moreover,LIVE/DEAD fluorescence test further confirmed that the composite PET could kill bacteria quickly and efiectively(within 30 min);while negligible cytotoxicity was observed to HSF and HUVEC *** eco-friendly fabrication of composite antibacterial PET was accomplished by on-line melt *** composite antibacterial PET has potential use in multiple fields to combat with pathogenic including textiles,packaging materials,decoration materials and biomedical devices,etc.

关键词： antibacterial polyester one-step eco-friendly method on-line amination reaction melt coextrusion cytocompatibility

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Pulse Amplification in Dispersion-Decreasing Fibers with Symbolic Computation

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Communications in Theoretical Physics 2009年第12期52卷 1076-1080页

作者： LIU Wen-Jun TIAN Bo XU Tao cai ke-Jie ZHANG huan School of Science Beijing University of Posts and Telecommunications P.O. Box 122 Beijing 100876 China State key Laboratory of Software Development Environment Beijing University of Aeronautics and Astronautics Beijing 100083 China key Laboratory of Information Photonics and Optical Communication （BUPT） Ministry of Education Beijing University of Posts and Telecommunications P.O. Box 128 Beijing 100876 China

The pulse amplification in the dispersion-decreasing fiber （DDF） is investigated via symbolic computation to solve the variable-coefficient higher-order nonlinear Schrfdinger equation with the effects of third-order dispersion, self-steepening, and stimulated Raman scattering. The analytic one-soliton solution of this model is obtained with a set of parametric conditions. Based on this solution, the fundamental soliton is shown to be amplified in the DDF. The comparison of the amplitude of pulses for different dispersion profiles of the DDF is also performed through the graphical analysis. The results of this paper would be of certain value to the study of signal amplification and pulse compression.

关键词： fundamental soliton pulse amplication variable-coefficient higher-order nonlinear Schrodingerequation symbolic computation dispersion-decreasing fiber

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Cyclic testing of moment-shear force interaction in reinforced concrete shear wall substructures

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Earthquake Engineering and Engineering Vibration 2020年第2期19卷 465-481页

作者： ke Du huan Luo Jingjiang Sun key Laboratory of Earthquake Engineering and Engineering Vibration Institute of Engineering MechanicsChina Earthquake AdministrationHarbin 150080China

Previous quasi-static cyclic tests of shear walls,which routinely used an incremental lateral displacement test protocol with a constant axial load,failed to reflect the character of moment-shear force interaction of prototype *** study the effect of the moment-shear force interaction on the seismic performance of shear walls,three identical 2-story shear wall specimens with different loading patterns were constructed at 1/2 scale,to represent the lower portion of an 11-story high-rise building,and were tested under reversed cyclic *** axial force,shear force and bending moment were simultaneously applied to simulate the effects of gravity loads and earthquake excitations on the *** axial force and bending moment delivered from the upper structure were applied to the top of the specimens by two vertical actuators,and the shear force was applied to the specimens by two horizontal actuators.A mixed force-displacement control test program was adopted to ensure that the bending moment and the lateral shear were increased *** experimental results show that the moment-shear force interaction had a significant effect on the failure pattern,hysteretic characteristics,ductility and energy dissipation of the *** is recommended that moment-shear force interaction should be considered in the loading condition of RC shear wall substructures cyclic tests.

关键词： shear walls quasi-static cyclic test moment-shear force interaction collapse test hysteretic curves forcedisplacement mixed control test

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Heuristics for Online Scheduling on Identical Parallel Machines with Two GoS Levels

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Journal of Systems Science & Complexity 2019年第4期32卷 1180-1193页

作者： cai Shuang LIU ke Logistics R&D Department Beijing Jingdong Zhenshi Information Technology Co.Ltd.Beijing 100176China Academy of Mathematics and Systems Science Chinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100190China

This paper considers the online scheduling problem on m(m≥3)parallel machines(the first k machines with grade 1 and the remaining m-k machines with grade 2)with two Go S levels and makespan as the objective *** jobs arrive over time with grade 1 or 2 and an arrival job can be assigned to a machine only when the grade of the job is no less than the grade of the *** cases are considered:(i)For k=1,the authors present an online algorithm with competitive ratio of9/5.(ii)For 1

关键词： Grade of Service(GoS)constraints heuristic algorithm online scheduling parallel machine scheduling

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