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Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

Horticultural Plant Journal 2024年第4期10卷 961-970页

作者： Yinqing Yang Lei Zhang Qi Tang Lingkui Zhang Xing Li Shumin chen Kang Zhang Ying Li Xilin Hou Feng cheng State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China State Key Laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China

Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so *** genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of ***,has been widely used as a common reference in biological *** its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 ***,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold ***,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS ***,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

关键词： Brassica oleracea Oxford nanopore technologies Gene annotation Alternative splicing

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KHK-A promotes fructose-dependent colorectal cancer liver metastasis by facilitating the phosphorylation and translocation of PKM2

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Acta Pharmaceutica Sinica B 2024年第7期14卷 2959-2976页

作者： Chaofan Peng Peng Yang Dongsheng Zhang Chi Jin Wen Peng Tuo Wang Qingyang Sun Zhihao chen Yifei Feng Yueming Sun Department of General Surgery the First Affiliated Hospital of Nanjing Medical UniversityNanjing 210029China Colorectal Institute of Nanjing Medical University Nanjing 210029China The First School of Clinical Medicine Nanjing Medical UniversityNanjing 210029China Jiangsu Province Engineering Research Center of Colorectal Cancer Precision Medicine and Translational Medicine Nanjing 210029China

Excessive fructose diet is closely associated with colorectal cancer(CRC)***,fructose’s specific function and precise mechanism in colorectal cancer liver metastasis(CRLM)is rarely ***,this study reported that the fructose absorbed by primary colorectal cancer could accelerate CRLM,and the expression of KHK-A,not KHK-C,in liver metastasis was higher than in paired primary ***,KHK-A facilitated fructose-dependent CRLM in vitro and in vivo by phosphorylating PKM2 at ***2 phosphorylated by KHK-A inhibited its tetramer formation and pyruvic acid kinase activity but promoted the nuclear accumulation of *** and aerobic glycolysis activated by nuclear PKM2 enhance CRC cells’migration ability and anoikis resistance during CRLM ***-46 treatment,targeting the phosphorylation of PKM2,inhibited the pro-metastatic effect of ***,c-myc activated by nuclear PKM2 promotes alternative splicing of KHK-A,forming a positive feedback loop.

关键词： CRC CRLM Fructose KHK-A PKM2

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Detection and analysis of landslide geomorphology based on UAV vertical photogrammetry

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Journal of Mountain Science 2024年第4期21卷 1190-1214页

作者： BI Rui GAN Shu YUAN Xiping LI Kun LI Raobo LUO Weidong chen cheng GAO Sha HU Lin ZHU Zhifu School of Land and Resources Engineering Kunming University of Science and TechnologyKunming 650093China Plication Engineering Research Center of Spatial Information Surveying and Mapping Technology in Plateau and Mountainous Areas Set by Universities in Yunnan Province Kunming 650093China West Yunnan University of Applied Sciences Key Laboratory of Mountain Real Scene Point Cloud Data Processing and Application for Universities in Yunnan ProvinceDali 671006China

High-resolution landslide images are required for detailed geomorphological analysis in complex topographic environment with steep and vertical landslide *** study proposed a vertical route planning method for unmanned aerial vehicles(UAVs),which could achieve rapid image collection based on strictly calculated route *** effectiveness of this method was verified using a DJI Mavic 2 Pro,obtaining high-resolution landslide images within the Dongchuan debris flow gully,in the Xiaojiang River Basin,Dongchuan District,Yunnan,China.A three-dimensional(3D)model was constructed by the structure-from-motion and multi-view stereo(SfM-MVS).Micro-geomorphic features were analyzed through visual interpretation,geographic information system(GIS),spatial analysis,and mathematical statistics *** results demonstrated that the proposed method could obtain comprehensive vertical information on landslides while improving measurement *** 3D model was constructed using the vertically oriented flight route to achieve centimeter-level accuracy(horizontal accuracy better than 6 cm,elevation accuracy better than 3 cm,and relative accuracy better than 3.5 cm).The UAV technology could further help understand the micro internal spatial and structural characteristics of landslides,facilitating intuitive acquisition of surface *** slope of landslide clusters ranged from 36°to 72°,with the majority of the slope facing east and *** elevation levels were relatively consistent while middle to lower elevation levels gradually decreased from left to right with significant variations in lower elevation *** the rainy season,surface runoff was abundant,and steep topography exacerbated changes in surface *** route method is suitable for unmanned aerial vehicle(UAV)landslide surveys in complex mountainous *** geomorphological analysis methods used will provide references for identifying and describing topographic

关键词： UAV Landslide Vertical route SfM-MVS Topographic features

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HEVC自适应去方块滤波器的VLSI设计与实现

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计算机辅助设计与图形学学报 2024年第4期36卷 636-644页

作者：陈焯淼陈志峰陈建汪家华福州大学物理与信息工程学院福州350116

去方块滤波是高效视频编码(HEVC)的重要组成部分,能够有效地改善编码图像的主观质量,是提升视频整体编码性能的重要手段之一.针对HEVC硬件编码器中去方块滤波技术复杂度较高的问题,为了在节省资源消耗的同时减少处理周期,改善滤波效率,... 详细信息

去方块滤波是高效视频编码(HEVC)的重要组成部分,能够有效地改善编码图像的主观质量,是提升视频整体编码性能的重要手段之一.针对HEVC硬件编码器中去方块滤波技术复杂度较高的问题,为了在节省资源消耗的同时减少处理周期,改善滤波效率,提出HEVC自适应去方块滤波的硬件算法和VLSI架构.首先基于HEVC编码结构的边界规则,提出一种无需递归循环计算的快速边界判断算法,降低硬件实现的复杂度;然后基于上述边界判断结果,提出一种可自主选择滤波边界进行去方块滤波的4级流水结构,减少滤波处理周期;最后将亮度和色度并行滤波,设计一种高度并行且兼容共享的存储架构,改善滤波效率且节约存储资源消耗.实验结果表明,在TSMC90 nm工艺下,所设计的去方块滤波结构的硬件面积比已有结构减少60%左右,并且最高能达到250 MHz的工作频率,可满足8K@60帧/s的超高清视频的实时编码.

关键词：高效视频编码去方块滤波边界判断硬件设计

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Single-cell transcriptomic analysis reveals transcript enrichment in oxidative phosphorylation,fluid sheer stress,and inflammatory pathways in obesity-related glomerulopathy

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Genes & Diseases 2024年第4期11卷 314-326页

作者： Yinyin chen Yushun Gong Jia Zou Guoli Li Fan Zhang Yiya Yang Yumei Liang Wenni Dai Liyu He Hengcheng Lu Department of Nephrology Hunan Provincial People's HospitalThe First Affliated Hospital of Hunan Normal UniversityHunan Clinical Research Center for Chronic Kidney DiseaseChangshaHunan 410000China Department of Nephrology The Second Xiangya Hospital of Central South UniversityHunan Key Laboratory of Kidney Disease and Blood PurificationChangshaHunan 410011China Cardiovascular Research Institute of Jiangxi Province Jiangxi Provincial People's HospitalThe First Affiliated Hospital of Nanchang Medical CollegeNanchangJiangxi 330006China

Obesity-related glomerulopathy(ORG)is an independent risk factor for chronic kid-ney disease and even progression to end-stage renal *** have been undertaken to elucidate the mechanisms underlying the development of ORG and substantial advances have been made in the treatment of ORG,but relatively little is known about cell-specific changes in gene *** define the transcriptomic landscape at single-cell resolution,we analyzed kidney samples from four patients with ORG and three obese control subjects without kidney disease using single-cell RNA *** report for the first time that immune cells,including T cells and B cells,are decreased in ORG *** analysis indicated that SPP1 was significantly up-regulated in T cells and B *** gene is related to inflammation and cell *** of differential gene expression in glomerular cells(endothelial cells,mesangial cells,and podocytes)showed that these cell types were mainly enriched in genes related to oxidative phosphorylation,cell adhesion,thermogenesis,and inflammatory pathways(PI3K-Akt signaling,MAPK signaling).Furthermore,we found that the podocytes of ORG patients were enriched in genes related to the fluid shear stress ***,an evaluation of cell-cell communications revealed that there were interactions between glomerular parietal epithelial cells and other cells in ORG patients,with major interactions between parietal epithelial cells and ***,our identification of molecular events,cell types,and differentially expressed genes may facilitate the development of new preventive or therapeutic approaches for ORG.

关键词： Fluid shear stress Inflammation Obesity-related glomerulopathy Oxidative phosphorylation Single-cell RNA seq

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Efficacy of ginseng-based Renshenguben oral solution for cancer-related fatigue among patients with advanced-stage hepatocellular carcinoma:A prospective multicenter cohort study

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Hepatobiliary & Pancreatic Diseases International 2024年第3期23卷 249-256页

作者： Ming-Da Wang chen Yuan Ke-Chun Wang Nan-Ya Wang Ying-Jian Liang Hong Zhu Xiang-Min Tong Tian Yang Department of Hepatobiliary and Pancreatic Surgery General Surgery CenterFirst Hospital of Jilin UniversityChangchun 130021China Department of Hepatobiliary Surgery Eastern Hepatobiliary Surgery HospitalSecond Military Medical University(Naval Medical University)Shanghai 200438China Department of Clinical Laboratory Laboratory Medicine CenterZhejiang Provincial People’s HospitalHangzhou Medical CollegeHangzhou 310000China Department of Hepatobiliary Surgery First Affiliated Hospital of Harbin Medical UniversityHarbin 150007China Department of Medical Oncology First Affiliated Hospital of Soochow UniversitySuzhou 215006China fDepartment of Central Laboratory Affiliated Hangzhou First People’s HospitalWestlake University School of MedicineHangzhou 310006China

Background:Cancer-related fatigue(CRF)is a common and debilitating symptom experienced by patients with advanced-stage cancer,especially those undergoing antitumor *** study aimed to evaluate the efficacy and safety of Renshenguben(RSGB)oral solution,a ginseng-based traditional Chinese medicine,in alleviating CRF in patients with advanced hepatocellular carcinoma(HCC)receiving antitumor ***:In this prospective,open-label,controlled,multicenter study,patients with advanced HCC at BCLC stage C and a brief fatigue inventory(BFI)score of≥4 were *** were assigned to the RSGB group(RSGB,10 mL twice daily)or the control group(with supportive care).Primary and secondary endpoints were the change in multidimensional fatigue inventory(MFI)score,and BFI and functional assessment of cancer therapy-hepatobiliary(FACT-Hep)scores at weeks 4 and 8 after *** events(AEs)and toxicities were ***:A total of 409 participants were enrolled,with 206 assigned to the RSGB *** week 4,there was a trend towards improvement,but the differences were not statistically *** week 8,the RSGB group exhibited a significantly lower MFI score(P<0.05)compared to the control group,indicating improved fatigue ***,the RSGB group showed significantly greater decrease in BFI and FACT-Hep scores at week 8(P<0.05).Subgroup analyses among patients receiving various antitumor treatments showed similar *** linear regression analyses revealed that the RSGB group experienced a significantly substantial decrease in MFI,BFI,and FACT-Hep scores at week *** serious drug-related AEs or toxicities were ***:RSGB oral solution effectively reduced CRF in patients with advanced HCC undergoing antitumor therapy over an eight-week period,with no discernible *** findings support the potential of RSGB oral solution as an adjunctive treatment for managing CRF in this patient population.

关键词： Cancer-related fatigue Hepatocellular carcinoma Renshenguben oral solution Efficacy Safety Ginseng

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An endophytic fungus interacts with the defensinlike protein OsCAL1 to regulate cadmium allocation in rice

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Molecular Plant 2024年第2期17卷 312-324页

作者： Tianyu Gu Ziai Qi Yating Wang Siying chen Jing Yan Huapeng Qiu Yanxuan Yu Zjun Fang Junmin Wang Jiming Gong National Key Laboratory of Plant Molecular Genetics Shanghai Center for Plant Stress BiologyCAS Center for Excellence in Molecular Plant SciencesChinese AcademyofSciencesShanghai200032China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China University of the Chinese Academy of Sciences Beijing 100049China Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization College of Life ScienceHunan University of Science and TechnologyXiangtan411201China State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China Institute of Crops and Nuclear Technology Utilization Zhejiang Academy of Agricultural SciencesHangzhou 310021China

Defensin-like proteins are conserved in multicellular organisms and contribute to innate immune re-sponses against fungal *** rice,defensins play a novel role in regulating cadmium(Cd)efflux from the ***,whether the antifungal activity of defensins correlates with Cd-efflux function remains *** this study,we isolated an endophytic Fusarium,designed Fo1o,by a comparative mi-crobiome analysis of rice plants grown in a paddy contaminated with ***10 is tolerant to high levels of Cd,but is sensitive to the defensin-like protein OsCAL1,which mediates Cd efflux to the *** found that Fo10 symbiosis in rice is regulated by OsCAL1 dynamics,and Fo10 coordinates multiple plant pro-cesses,including Cd uptake,vacuolar sequestration,efflux to the environment,and formation of Fe pla-ques in the *** processes are dependent on the salicylic acid signaling pathway to keep Cd levels low in the cytosol of rice cells and to decrease Cd levels in rice grains without any yield ***10 also plays a role in Cd tolerance in the poaceous crop maize and wheat,but has no observed effects in the eudicot plants Arabidopsis and *** together,these findings provide insights into the mech-anistic basis underlying how afungal endophyte and host plant interact to control Cd accumulation in host plants by adapting defense responses to promotethe establishment ofa symbiosis that permits adaptation to high-Cd environments.

关键词： defensin-like protein Fusarium oxysporum endophyte cadmium allocation

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Grain Yield,Biomass Accumulation,and Leaf Photosynthetic Characteristics of Rice under Combined Salinity-Drought Stress

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Rice science 2024年第1期31卷 118-128,I0023页

作者： WEI Huanhe GENG Xiaoyu ZHANG Xiang ZHU Wang ZHANG Xubin chen Yinglong HUO Zhongyang ZHOU Guisheng MENG Tianyao DAI Qigen Jiangsu Key Laboratory of Crop Cultivation and Physiology/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Saline-Alkali Soil Reclamation and Utilization in Coastal Areas the Ministry of Agriculture and Rural Affairs of China/Research Institute of Rice Industrial Engineering TechnologyYangzhou UniversityYangzhou 225009China Institute of Agricultural Science and Technology Development/Joint International Research Laboratory of Agriculture and Agri-Product Safety the Ministry of Education of ChinaYangzhou UniversityYangzhou 225009China

Simultaneous stresses of salinity and drought often coincide during rice-growing seasons in saline lands,primarily due to insufficient water resources and inadequate irrigation ***,combined salinity-drought stress poses a major threat to rice *** this study,two salinity levels(NS,non-salinity;HS,high salinity)along with three drought treatments(CC,control condition;DJ,drought stress imposed at jointing;DH,drought stress imposed at heading)were performed to investigate their combined influences on leaf photosynthetic characteristics,biomass accumulation,and rice yield ***,drought,and their combination led to a shortened growth period from heading to maturity,resulting in a reduced overall growth *** yield was reduced under both salinity and drought stress,with a more substantial reduction under the combined salinity-drought *** combined stress imposed at heading caused greater yield losses in rice compared with the stress imposed at ***,the combined salinity-drought stress induced greater decreases in shoot biomass accumulation from heading to maturity,as well as in shoot biomass and nonstructural carbohydrate(NSC)content in the stem at heading and ***,it increased the harvest index and NSC remobilization *** and drought reduced the leaf area index and SPAD value of flag leaves and weakened the leaf photosynthetic characteristics as indicated by lower photosynthetic rates,transpiration rates,and stomatal *** reductions were more pronounced under the combined ***,drought,and especially their combination,decreased the activities of ascorbate peroxidase,catalase,and superoxide dismutase,while increasing the contents of malondialdehyde,hydrogen peroxide,and superoxide *** results indicated a more significant yield loss in rice when subjected to combined salinity-drought *** individual and combined stresses of salinity and dro

关键词： antioxidant defense system combined salinity-drought stress drought stress photosynthetic characteristics rice salinity stress

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A rapid field crop data collection method for complexity cropping patterns using UAV and YOLOv3

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Frontiers of Earth Science 2024年第1期18卷 242-255页

作者： Huifang ZHANG Binyao WANG Zhonggang TANG Jiahui XUE Ruihang chen Hongcheng KAN Shumiao LU Lina FENG Ye HE Shuhua YI Institute of Fragile Eco-environment Nantong UniversityNantong 226019China School of Geographic Science Nantong UniversityNantong 226019China Nantong Key Laboratory of Spatial Information Technology R&D and Application School of Geographic ScienceNantong UniversityNantong 226019China

Crop type mapping using remote sensing is critical for global agricultural monitoring and food ***,the complexity of crop planting patternsand spatial heterogeneity pose significant challenges to field data collection,thereby limiting the accuracy of remotely sensed crop *** study proposed a new approach for rapidly collecting field crop data by integrating unmanned aerial vehicle(UAV)images with the YOLOv3(You Only Look Once version 3)*** impacts of UAV flight altitude and the number of training samples on the accuracy of crop identification models were investigated using peanut,soybean,and maize as *** results showed that the average Fl-score for crop type detection accuracy reached 0.91 when utilizing UAV images captured at an altitude of 20 *** addition,a positive correlation was observed between identification accuracy and the number of training *** model developed in this study can rapidly and automatically identify crop types from UAV images,which significantly improves the survey efficiency and provides an innovative solution for acquiring field crop data in large areas.

关键词： deep learning flight altitude crop survey peanut soybean maize

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Ecological problems and ecological restoration zoning of the Aral Sea

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Journal of Arid Land 2024年第3期16卷 315-330页

作者： BAO Anming YU Tao XU Wenqiang LEI Jiaqiang JIAPAER Guli chen Xi Tojibaev KOMILJON Shomurodov KHABIBULLO Xabibullaev B SAGIDULLAEVICH Idirisov KAMALATDIN State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqi 830011China Key Laboratory of GIS&RS Application Xinjiang Uygur Autonomous RegionUrumqi 830011China University of Chinese Academy of Sciences Beijing 100049China CAS Research Center for Ecology and Environment of Central Asia Urumqi 830011China Institute of Botany of the Academy of Sciences of the Republic of Uzbekistan Tashkent 100125Uzbekistan International Innovation Center for Aral Sea Basin under the President of the Republic of Uzbekistan Nukus 230100Uzbekistan

The Aral Sea was the fourth largest lake in the world but it has shrunk dramatically as a result of irrational human activities, triggering the "Aral Sea ecological crisis". The ecological problems of the Aral Sea have attracted widespread attention, and the alleviation of the Aral Sea ecological crisis has reached a consensus among the five Central Asian countries(Kazakhstan, Uzbekistan, Tajikistan, Kyrgyzstan, and Turkmenistan). In the past decades, many ecological management measures have been implemented for the ecological restoration of the Aral Sea. However, due to the lack of regional planning and zoning, the results are not ideal. In this study, we mapped the ecological zoning of the Aral Sea from the perspective of ecological restoration based on soil type, soil salinity, surface water, groundwater table, Normalized Difference Vegetation Index(NDVI), land cover, and aerosol optical depth(AOD) data. Soil salinization and salt dust are the most prominent ecological problems in the Aral Sea. We divided the Aral Sea into 7 first-level ecological restoration subregions(North Aral Sea catchment area in the downstream of the Syr Darya River(Subregion Ⅰ);artificial flood overflow area in the downstream of the Aral Sea(Subregion Ⅱ);physical/chemical remediation area of the salt dust source area in the eastern part of the South Aral Sea(Subregion Ⅲ);physical/chemical remediation area of severe salinization in the central part of the South Aral Sea(Subregion Ⅳ);existing water surface and potential restoration area of the South Aral Sea(Subregion Ⅴ);Aral Sea vegetation natural recovery area(Subregion Ⅵ);and vegetation planting area with slight salinization in the South Aral Sea(Subregion Ⅶ)) and 14 second-level ecological restoration subregions according to the ecological zoning principles. Implementable measures are proposed for each ecological restoration subregion. For Subregion Ⅰ and Subregion Ⅱ with lower elevations, artificial flooding should be carried out to re

关键词： ecological restoration zoning salt and dust storms soil salinization ecological crisis Aral Sea Central Asia

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