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A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding

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Molecular Plant 2022年第8期15卷 1268-1284页

作者： Yun Deng shoucheng liu Yilin Zhang Jingsheng Tan Xiaopeng Li Xiao Chu Binghua Xu Yao Tian Yudong Sun Bosheng Li YunbiXu Xing Wang Deng Hang He Xingping Zhang Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences at WeifangWeifangShandong 261000China School of Advanced Agricultural Sciences and School of Life Sciences State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijing 100871China Jiangsu Xuhuai Area Huaiyin Institute of Agricultural Science HuaianJiangsu 223300China

Watermelon,Citrullus lanatus,is the world's third largest fruit crop.Reference genomes with gaps and a narrow genetic base hinder functional genomics and genetic improvement of watermelon.Here,we report the assembly of a telomere-to-telomere gap-free genome of the elite watermelon inbred line G42 by incorporating high-coverage and accurate long-read sequencing data with multiple assembly strategies.All 11 chromosomes have been assembled into single-contig pseudomolecules without gaps,representing the highest completeness and assembly quality to date.The G42 reference genome is 369321829 bp in length and contains 24205 predicted protein-coding genes,with all 22 telomeres and 11 centromeres characterized.Furthermore,we established a pollen-EMS mutagenesis protocol and obtained over 200000M1 seeds from G42.In a sampling pool,48 monogenic phenotypic mutations,selected from 223M1and 78 M2 mutants with morphological changes,were confirmed.The average mutation density was 1 SNP/1.69Mband1 indel/4.55 Mb per M1 plant and 1SNP/1.08Mb and 1 indel/6.25 Mb per M2 plant.Taking advantage of the gap-free G42 genome,8039 mutations from 32 plants sampled from M1 and M2 families were identified with 100%accuracy,whereas only 25% of the randomly selected mutations identified using the 97103v2 reference genome could be confirmed.Using this library and the gap-free genome,two genes responsible for elongated fruit shape and male sterility(CiMs1)were identified,both caused by a single basechange from G to A.The validated gap-free genome and its EMS mutation library provide invaluable resources for functional genomics and genetic improvement of watermelon.

关键词： watermelon gap-free genome EMS,mutation library gene discovery genome-wide sequencing genic male sterility

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Identification and analysis of mouse non-coding RNA using transcriptome data

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Science China(Life Sciences) 2016年第9期59卷 589-603页

作者： Yuhui Zhao Wanfei liu Jingyao Zeng shoucheng liu Xinyu Tan Hasanawad Aljohi Songnian Hu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China University of Chinese Academy of Sciences Beijing 100049 China Joint Center for Genomics Research (JCGR) King Abdulaziz City for Science and Technology and Chinese Academy of Sciences Riyadh 11442 Saudi Arabia

Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel c DNA sequencing(RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs, especially linc RNAs, have been widely identified and well characterized as important regulators of diverse biological processes. In this study, we used ultra-deep RNA-seq data from 15 mouse tissues to study the diversity and dynamic of non-coding RNAs in mouse. Using our own criteria, we identified totally 16,249 non-coding genes(21,569 non-coding RNAs) in mouse. We annotated these non-coding RNAs by diverse properties and found non-coding RNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these non-coding RNAs show significant enrichment with transcriptional initiation and elongation signals including histone modifications(H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The gene set enrichment analysis(GSEA) result revealed several sets of linc RNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction. Taken together, this study provides a more comprehensive annotation of mouse non-coding RNAs and gives an opportunity for future functional and evolutionary study of mouse non-coding RNAs.

关键词：非编码RNA 转录表达小鼠蛋白编码基因组织特异性识别组数生物过程

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Effectiveness and safety of acupuncture in treatment of pregnancyrelated symptoms:a systematic review and Meta-analysis

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Journal of Traditional Chinese Medicine 2024年第1期44卷 16-26页

作者： liu Tingting liu Tongou liu Mingfu School of Traditional Chinese Medicine Clinical Medicine Hubei University of Traditional Chinese MedicineWuhan 430000China First Clinical College of Hubei University of Traditional Chinese Medicine Wuhan 430000China Department of Acupuncture and Tuina Affiliated Hospital of Hubei University of Traditional Chinese MedicineHubei Provincial Hospital of Traditional Chinese MedicineWuhan 430000China

OBJECTIVE:To systematically evaluate the efficacy and safety of acupuncture(AM)in the treatment of pregnancyrelated symptoms such as acute vomiting during pregnancy.METHODS:We comprehensively searched the available literature up to November 2021,including Pub Med,Embase,Cochrane Library,Chinese Biomedical Literature Database,and China National Knowledge Infrastructure Database,for randomized controlled trials(RCTs)on AM for the treatment of severe vomiting,insomnia,pharyngeal and pelvic pain,mood abnormalities,and dyspepsia during pregnancy.RESULTS:Sixteen RCTs with a cumulative sample size of 1178 cases were included.Of these,964 patients were included in the Meta-analysis.The Meta-analysis results showed that AM was more efficient than Western medicine in treating discomfort during pregnancy[odds ratio(OR)=1.19,95%confidence interval(CI)(1.11,1.28),P<0.01].AM was better than the control group in improving the visual analog scale scores[standard mean difference(SMD)=0.62,95%CI(0.53,0.71),P<0.01].AM was superior to the control group in improving Numerical Rating Scale(NRS)symptom scores[OR=7.31,95%CI(3.36,15.94),P<0.01].There was no significant difference in adverse effects between the AM and sham-AM groups and the analgesic drug group[OR=0.70,95%CI(0.39,1.28),P=0.25],but the treatment and control groups had mild adverse effects with a low incidence.CONCLUSIONS:AM is more effective than other treatments or pharmacotherapy alone in the treatment of pregnancy-related symptoms,and is relatively safe.However,the quality of the included trials was rather poor,and high-quality studies are required to confirm our findings.

关键词： acupuncture pregnancy nausea vomiting sleep initiation and maintenance disorders low back pain pelvic pain mood abnormalities Meta-analysis systematic review

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Removal of Cr(Ⅵ)by glutaraldehyde-crosslinked chitosan encapsulating microscale zero-valent iron:Synthesis,mechanism,and longevity

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Journal of Environmental Sciences 2024年第8期142卷 115-128页

作者： Yijun Duan Fang liu Xiang liu Miao Li School of Environment Tsinghua UniversityBeijing 100084China Transportation Institute of Inner Mongolia University Hohhot 010070China

Microscale zero-valent iron(mZVI)has shown great potential for groundwater Cr(Ⅵ)remediation.However,low Cr(Ⅵ)removal capacity caused by passivation restricted the wide use of mZVI.We prepared mZVI/GCS by encapsulating mZVI in a porous glutaraldehydecrosslinked chitosan matrix,and the formation of the passivation layer was alleviated by reducing the contact between zero-valent iron particles.The average pore diameter of mZVI/GCS was 8.775 nm,which confirmed the mesoporous characteristic of this material.Results of batch experiments demonstrated that mZVI/GCS exhibited high Cr(Ⅵ)removal efficiency in a wide range of pH(2-10)and temperature(5-35℃).Common groundwater coexisting ions slightly affected m ZVI/GCS.The material showed great reusability,and the average Cr(Ⅵ)removal efficiency was 90.41%during eight cycles.In this study,we also conducted kinetics and isotherms analysis.Pseudo-second-order model was the most matched kinetics model.The Cr(Ⅵ)adsorption process was fitted by both Langmuir and Freundlich isotherms models,and the maximum Langmuir adsorption capacity of m ZVI/GCS reached243.63 mg/g,which is higher than the adsorption capacities of materials reported in most of the previous studies.Notably,the column capacity for Cr(Ⅵ)removal of a mZVI/GCS-packed column was 6.4 times higher than that of a mZVI-packed column in a 50-day experiment.Therefore,mZVI/GCS with a porous structure effectively relieved passivation problems of mZVI and showed practical application prospects as groundwater Cr(Ⅵ)remediation material with practical application prospects.

关键词： Chitosan Glutaraldehyde mZVI Cr(Ⅵ) Groundwater

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Frequency Regulation of VSC-MTDC System with Offshore Wind Farms

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Journal of Modern Power Systems and Clean Energy 2024年第1期12卷 275-286页

作者： Haoyu liu Chongru liu North China Electric Power University Beijing 102206China

Frequency regulation of voltage source converter-based multi-terminal high-voltage direct current(VSC-MTDC)system with offshore wind farms enhances the frequency stability by compensating the power for a disturbed AC system.However,it is difficult to reasonably allocate frequency-regulation resources due to a lack of coordination mechanisms between wind farms and the MTDC system.Moreover,it is difficult for the frequency control of the wind farms to manage changes in wind speed;and the risk of wind-turbine stalls is high.Thus,based on the kinetic energy of wind turbines and the power margin of the converters,the frequency-regulation capability of wind turbines is evaluated,and a dynamic frequency-support scheme considering the real-time frequency-support capability of the wind turbines and system frequency evolution is proposed to improve the frequency-support performance.A power adaptation technique at variable wind speeds is developed;the active power in the frequency-support stage and restoration stage is switched according to the wind speed.A hierarchical zoning frequency-regulation scheme is designed to use the frequency-regulation resources of different links in the MTDC system with wind farms.The simulation results show that the novel frequency-regulation strategy maintains frequency stability with wind-speed changes and avoids multiple frequency dips.

关键词： Wind generation voltage source converter-based multi-terminal high-voltage direct current(VSC-MTDC) frequency regulation cooperative control adaptive control variable wind speed

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Characteristics and sources of peroxyacetyl nitrate(PAN)in the rural North China Plain:Results from1-year continuous observations

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Journal of Environmental Sciences 2024年第4期138卷 719-731页

作者： Xin liu Xiaowei He Chenglong Zhang Yifei Song Shuyang Xie Chengtang liu Pengfei liu Yuanyuan Zhang Yujing Mu Junfeng liu Research Center for Eco-Environmental Sciences Chinese Academy of SciencesBeijing 100085China University of Chinese Academy of Sciences Beijing 100049China

Peroxyacetyl nitrate(PAN)is an important photochemical pollutant in the troposphere,whereas long-term measurements are scarce in rural areas in North China Plain(NCP),resulting in unclear seasonal variations and sources of PAN in rural NCP.In this study,we conducted a 1-year observation of PAN during 2021-2022 at the rural NCP site.The average concentrations of PAN were 1.10,0.75,0.65,and 0.88 ppbv in spring,summer,autumn,and winter,respectively,with a 1-year average of 0.81±0.60 ppbv.Calculations indicate that the loss of PAN through thermal decomposition in summer accounts for 43.2% of the total formed PAN,which is an important reason for the low concentration of PAN in summer.We speculate that since the correlation between PAN and O_(3) in winter is significantly lower than that in other seasons,the observed regional transport of PAN cannot be ignored in winter.Through budget analysis,regional transport accounted for 12.8% and 55.9% of the observed PAN on the spring and winter pollution days,respectively,which showed that regional transport played key roles during the photochemical pollution of the rural NCP in winter.The potential source contribution function revealed that the transported PAN mainly comes from southern Hebei in spring.In winter,the transported PAN was mainly from Langfang,Hengshui,and southern Beijing.Our findings may aid in understanding PAN variations in different seasons in rural areas and highlight the impact of regional transport on the PAN budget.

关键词： Photochemical pollution Peroxyacetyl nitrate(PAN) Seasonal variations Regional transport Rural area

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High-performance,stable CoNi LDH@Ni foam composite membrane with innovative peroxymonosulfate activation for 2,4-dichlorophenol destruction

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Journal of Environmental Sciences 2024年第7期141卷 235-248页

作者： Yu liu Weibao liu Xinrui Gan Jiangwei Shang Xiuwen Cheng College of Chemistry and Environmental Science Xinjiang Laboratory of Phase Transitions and Microstructures of Condensed Matter PhysicsYili Normal UniversityYining 835000China Key Laboratory for Environmental Pollution Prediction and Control Gansu ProvinceCollege of Earth and Environmental SciencesLanzhou UniversityLanzhou 730000China

In this study,the cobalt-nickel layered double hydroxides(CoNi LDH)were synthesized with a variety of Co/Ni mass ratio,as CoxNiyLDHs.In comparison,Co1Ni3LDH presented the best peroxymonosulfate(PMS)activation efficiency for 2,4-dichlorophenol removal.Meanwhile,CoNi LDH@Nickel foam(CoNi LDH@NF)composite membrane was constructed for enhancing the stability of catalytic performance.Herein,CoNi LDH@NF-PMS system exerted high degradation efficiency of 99.22%within 90 min for 2,4-DCP when[PMS]_(0)=0.4 g/L,Co^(1)Ni^(3)LDH@NF=2 cm×2 cm(0.2 g/L),reaction temperature=298 K.For the surface morphology and structure of the catalyst,it was demonstrated that the CoNi LDH@NF composite membrane possessed abundant cavity structure,good specific surface area and sufficient active sites.Importantly,·OH,SO_(4)·^(-)and^(1)O_(2)played the primary role in the CoNi LDH@NF-PMS system for 2,4-DCP decomposition,which revealed the PMS activation mechanism in CoNi LDH@NF-PMS system.Hence,this study eliminated the stability and adaptability of CoNi LDH@NF composite membrane,proposing a new theoretical basis of PMS heterogeneous catalysts selection.

关键词： CoNi LDH@NF composite membrane Peroxymonosulfate 2,4-dichlorophenol Reactive radicals

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A Novel Design of a Pre-separation Panel Structure to Protect Against the Impact of an Explosion in an Aircraft Plenum Chamber

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Acta Mechanica Solida Sinica 2024年第1期37卷 166-180页

作者： Zongxing liu Xiang Yang Jun liu School of Aeronautics Northwestern Polytechnical UniversityXi'an 710072China COMAC Shanghai Aircraft Design and Research Institute Shanghai 201210China

To reduce the damage of the pressurizing panel structure of a fuselage caused by an explosion at the“least risk bomb location”in an aircraft structure,a new pre-separation panel structure was designed to resist blast loading.First,the dynamic strain response and morphology of impact damage of the new pre-separation panel were measured in an impact damage test.Second,the commercial software LS-DYNA was used to calculate the propagation of the blast shock wave,and the results were compared with empirical equations to verify the rationality of the numerical calculation method.Finally,the fluid–structure coupling method was used to calculate the damage process of the pre-separation panel structure under the impact of an explosion wave and an impact block.The calculated results were in good agreement with the test results,which showed the rationality of the calculation method and the model.The residual strength of the damaged pre-separation panel was significantly higher than that of the original damaged panel.The results show that the new pre-separation panel structure is reasonable and has certain significance for guiding the design of plenum chambers with strong resistance to implosion for aircraft fuselages.

关键词： Pre-separation panel structure Explosive response Residual strength Aircraft plenum chamber Least risk bomb location

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Transplantation of fibrin-thrombin encapsulated human induced neural stem cells promotes functional recovery of spinal cord injury rats through modulation of the microenvironment

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Neural Regeneration Research 2024年第2期19卷 440-446页

作者： Sumei liu Baoguo liu Qian Li Tianqi Zheng Bochao liu Mo Li Zhiguo Chen Cell Therapy Center Beijing Institute of GeriatricsXuanwu HospitalCapital Medical UniversityNational Clinical Research Center for Geriatric Diseasesand Key Laboratory of Neurodegenerative DiseasesMinistry of EducationBeijingChina Center of Neural Injury and Repair Beijing Institute for Brain DisordersBeijingChina Center of Parkinson’s Disease Beijing Institute for Brain DisordersBeijingChina

Recent studies have mostly focused on engraftment of cells at the lesioned spinal cord,with the expectation that differentiated neurons facilitate recovery.Only a few studies have attempted to use transplanted cells and/or biomaterials as major modulators of the spinal cord injury microenvironment.Here,we aimed to investigate the role of microenvironment modulation by cell graft on functional recovery after spinal cord injury.Induced neural stem cells reprogrammed from human peripheral blood mononuclear cells,and/or thrombin plus fibrinogen,were transplanted into the lesion site of an immunosuppressed rat spinal cord injury model.Basso,Beattie and Bresnahan score,electrophysiological function,and immunofluorescence/histological analyses showed that transplantation facilitates motor and electrophysiological function,reduces lesion volume,and promotes axonal neurofilament expression at the lesion core.Examination of the graft and niche components revealed that although the graft only survived for a relatively short period(up to 15 days),it still had a crucial impact on the microenvironment.Altogether,induced neural stem cells and human fibrin reduced the number of infiltrated immune cells,biased microglia towards a regenerative M2 phenotype,and changed the cytokine expression profile at the lesion site.Graft-induced changes of the microenvironment during the acute and subacute stages might have disrupted the inflammatory cascade chain reactions,which may have exerted a long-term impact on the functional recovery of spinal cord injury rats.

关键词： biomaterial fibrinogen functional recovery induced neural stem cell transplantation microenvironment microglia spinal cord injury thrombin

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纤维增强混凝土预制隧道管片结构性能研究

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施工技术（中英文） 2024年第9期53卷 18-22页

作者：刘守成中铁十一局集团第二工程有限公司陕西西安712000

为研究纤维增强混凝土预制隧道管片抗弯性能、抗裂性能及隧道掘进机产生的推力对管片的影响,对钢筋混凝土管片和纤维增强混凝土管片进行全尺寸试验,包括静载弯曲试验和点荷载试验。研究结果表明,从设计荷载角度考虑,纤维增强混凝土管片... 详细信息

为研究纤维增强混凝土预制隧道管片抗弯性能、抗裂性能及隧道掘进机产生的推力对管片的影响,对钢筋混凝土管片和纤维增强混凝土管片进行全尺寸试验,包括静载弯曲试验和点荷载试验。研究结果表明,从设计荷载角度考虑,纤维增强混凝土管片相对于钢筋混凝土管片具有更高的承载力;钢筋混凝土管片和纤维增强混凝土管片点荷载⁃位移关系曲线变化趋势较相似,管片均未发生明显的开裂,均能承受设计荷载作用;与钢筋混凝土管片相比,纤维增强混凝土管片具有更好的抗弯性能和抗裂性能,纤维增强混凝土可替代钢筋混凝土制备预制隧道管片。

关键词：隧道管片混凝土预制试验研究

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