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Discriminative low-rank embedding with manifold constraint for image feature extraction and classification

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Optoelectronics Letters 2024年第5期20卷 299-306页

作者： YAN Chunman WEI shuhong School of Physics and Electronic Engineering Northwest Normal UniversityLanzhou 730070China Engineering Research Center of Gansu Province for Intelligent Information Technology and Application Lanzhou 730070China

The robustness against noise, outliers, and corruption is a crucial issue in image feature extraction. To address this concern, this paper proposes a discriminative low-rank embedding image feature extraction algorithm. Firstly, to enhance the discriminative power of the extracted features, a discriminative term is introduced using label information, obtaining global discriminative information and learning an optimal projection matrix for data dimensionality reduction. Secondly, manifold constraints are incorporated, unifying low-rank embedding and manifold constraints into a single framework to capture the geometric structure of local manifolds while considering both local and global information. Finally, test samples are projected into a lower-dimensional space for classification. Experimental results demonstrate that the proposed method achieves classification accuracies of 95.62%, 95.22%, 86.38%, and 86.54% on the ORL, CMUPIE, AR, and COIL20 datasets, respectively, outperforming dimensionality reduction-based image feature extraction algorithms.

关键词： manifold embedding dimensionality

Identification and fine mapping of qSW2 for leaf slow wilting in soybean

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The Crop Journal 2024年第1期12卷 244-251页

作者： Shengyou Li Changling Wang Chunjuan Yan Xugang Sun Lijun Zhang Yongqiang Cao Wenbin Wang shuhong Song Institute of Crop Research Liaoning Academy of Agricultural SciencesShenyang 110161LiaoningChina

Drought is one of the abiotic stresses limiting the production of soybean(Glycine max).Elucidation of the genetic and molecular basis of the slow-wilting(SW)trait of this crop offers the prospect of its genetic improvement.A panel of 188 accessions and a set of recombinant inbred lines produced from a cross between cultivars Liaodou 14 and Liaodou 21 were used to identify quantitative-trait loci(QTL)associated with SW.Plants were genotyped by Specific-locus amplified fragment sequencing and seedling leaf wilting was assessed under three water-stress treatments.A genome-wide association study identified 26 SW-associated single-nucleotide polymorphisms(SNPs),including three located in a 248-kb linkage-disequilibrium(LD)block on chromosome 2.Linkage mapping revealed a major-effect QTL,qSW2,associated with all three treatments and adjacent to the LD block.Fine mapping in a BC_(2)F_(3) population derived from a backcross between Liaodou 21 and R26 confined qSW2 to a 60-kb interval.Gene expression and sequence variation analysis identified the gene Glyma.02 g218100,encoding an auxin transcription factor,as a candidate gene for qSW2.Our results will contribute significantly to improving drought-resistant soybean cultivars by providing genetic information and resources.

关键词： Drought GWAS Linkage mapping Slow wilting Soybean(Glycine max)

Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

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Journal of Genetics and Genomics 2024年第4期51卷 394-406页

作者： Xin Li Quan Liu Chong Fu Mengxun Li Changchun Li Xinyun Li shuhong Zhao Zhuqing Zheng Key Lab of Agricultural Animal Genetics Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of AgricultureCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanHubei 430070China Institute of Agricultural Biotechnology Jingchu University of TechnologyJingmenHubei 448000China The Cooperative Innovation Center for Sustainable Pig Production WuhanHubei 430070China Hubei Hongshan Laboratory WuhanHubei 430070China

Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic variation.Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes,we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes.Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation.Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements.We identify that the genotypes of two DELs(296-bp DEL,chr7:52,172,101e52,172,397;278-bp DEL,chr18:23,840,143 e23,840,421)located in muscle-specific enhancers are associated with the expression of target genes related to meat quality(FSD2)and muscle fiber hypertrophy(LMOD2 and WASL)in pigs.Our results highlight the role of SVs in domestic porcine evolution,and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.

关键词： Pigs Structural variation Selection signatures Regulatory elements

Association between plasma growth differentiation factor 15 levels and pre-eclampsia in China

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Chronic Diseases and Translational Medicine 2024年第2期10卷 140-145页

作者： shuhong Xu Yicheng Lu Mengxin Yao Zhuoqiao yang Yan Chen Yaling Ding Yue Xiao Fei Liang Jiani Qian Jinchun Ma Songliang Liu Shilan Yan Jieyun Yin Qiuping Ma Taicang Affiliated Hospital of Soochow University The First People's Hospital of TaiCangSoochow UniversitySuzhouJiangsuChina Department of Epidemiology and Health Statistic Jiangsu Key Laboratory of Preventive and Translational Medicine for Major Chronic Non-communicable DiseasesSuzhou Medical College of Soochow UniversitySuzhouJiangsuChina Changshu Hospital Affiliated to Nanjing University of Chinese Medicine SuzhouJiangsuChina Department of Chronic Disease Gusu Center for Disease Control and PreventionSuzhouJiangsuChina Huzhou First People's Hospital HuzhouZhejiangChina

Background Growth differentiation factor-15(GDF-15)is a stress response protein and is related to cardiovascular diseases(CVD).This study aimed to investigate the association between GDF-15 and pre-eclampsia(PE).Method The study involved 299 pregnant women,out of which 236 had normal pregnancies,while 63 participants had PE.Maternal serum levels of GDF-15 were measured by using enzyme-linked immunosorbent assay kits and then translated into multiple of median(MOM)to avoid the influence of gestational week at blood sampling.Logistic models were performed to estimate the association between GDF-15 MOM and PE,presenting as odd ratios(ORs)and 95%confidence intervals(CIs).Results MOM of GDF-15 in PE participants was higher compared with controls(1.588 vs.1.000,p1)had a 4.74-fold(95%CI=2.23–10.08,p<0.001)increased risk of PE,adjusted by age,preconceptional body mass index,gravidity,and parity.Conclusions These results demonstrated that higher levels of serum GDF-15 were associated with PE.GDF-15 may serve as a biomarker for diagnosing PE.

关键词： growth differentiation factor 15 macrophage inhibiting cytokine 1 pre-eclampsia

Exploration of the dynamic water resource carrying capacity of the Keriya River Basin on the southern margin of the Taklimakan Desert,China

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Regional Sustainability 2021年第1期2卷 73-82页

作者： shuhong yang Tao yang State Key Iaboratbry of Desrt and Oasis Eolog Xinjiang Instinute of Rcology and GeographyChinese Academy of ScincesUrumqi830011China Univesity of Chinese Acadeny of Sciences Beijing 100101 China State Key ILaboratory of Hydrology Water Resources and Hydraulic Enginering Hohai University Nanjing 210098China

The water resource carrying capacity(WRCC)in river basin changes dynamically under climate change,economic development,and technological advancement.Climate change affects hydrological processes and spatial/temporal distribution of water resources;while economic develo-ment and technological advancement can also affect the balance of water resources systems.Under climate change,economic development,and technological advancement,itis of great significance to explore the dynamic behavior of WRCC in river basins.This will help to alleviate water resources security issues and build a sustainable water resources system.This study was carried out to evaluate the dynamic WRCC using the"climate,economics,and technology-control objective inversion mode",which used total water consumption,water-use efficiency,and restrained total pollutant control in the water functional area as boundary conditions.This study was conducted on the Keriya River Basin,a sub-catchment located in southem margin of the Taklimakan Desert.The WRCC in the Keriya River Basin in 2015 was calculated,and the trends in the short term(2020),middle tem(2030),and long term(2050)were predicted.The results revealed that climate change factors have a positive effect on WRCC in the Keriya River Basin,which leads to an increase in total water resources.Economic and technological development exhibits an overall positive effect,while increasing in water consumption and sewage discharge exhibit a negative effect.

关键词： Climate change Economic development Technological advancement Water resource carrying capacity Keriya River Basin

Hi-Tag:a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers

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Science China(Life Sciences) 2024年第5期67卷 1027-1034页

作者： Xiaolong Qi Lu Zhang Qiulin Zhao Peng Zhou Sai Xian Zhang Jingjin Li Zhuqing Zheng Yue Xiang Xueting Dai Zhe Jin Yaobang Jian Xinyun Li Liangliang Fu shuhong Zhao Key Lab of Agricultural Animal Genetics Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of AgricultureCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China The Cooperative Innovation Center for Sustainable Pig Production Wuhan 430070China Hubei Hongshan Laboratory Frontiers Science Center for Animal Breeding and Sustainable ProductionWuhan 430070China

Protein-mediated chromatin interactions can be revealed by coupling proximity-based ligation with chromatin immunoprecipitation.However,these techniques require complex experimental procedures and millions of cells per experiment,which limits their widespread application in life science research.Here,we develop a novel method,Hi-Tag,that identifies high-resolution,long-range chromatin interactions through transposase tagmentation and chromatin proximity ligation(with a phosphorothioate-modified linker).Hi-Tag can be implemented using as few as 100,000 cells,involving simple experimental procedures that can be completed within 1.5 days.Meanwhile,Hi-Tag is capable of using its own data to identify the binding sites of specific proteins,based on which,it can acquire accurate interaction information.Our results suggest that Hi-Tag has great potential for advancing chromatin interaction studies,particularly in the context of limited cell availability.

关键词： Hi-Tag chromatin interactions transposase tagmentation chromatin proximity ligation low cell numbers

Restoring periodontal tissue homoeostasis prevents cognitive decline by reducing the number of Serpina3nhigh astrocytes in the hippocampus

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The Innovation 2024年第1期5卷 98-108页

作者： Zongshan Shen shuhong Kuang Yong Zhang Jiayao Chen Shuting Wang Congfei Xu Yunjia Huang Min Zhang Shuheng Huang Jun Wang ChuanJiang Zhao Zhengmei Lin Xuetao Shi Bin Cheng Hospital of Stomatology Guangdong Provincial Key Laboratory of StomatologyGuanghua School of StomatologySun Yat-sen UniversityGuangzhou 510060China National Engineering Research Centre for Tissue Restoration and Reconstruction South China University of TechnologyGuangzhou 510006China Key Laboratory of Biomedical Engineering of Guangdong Province South China University of TechnologyGuangzhou 510006China School of Biomedical Science and Engineering South China University of TechnologyGuangzhou 510650China The First Affiliated Hospital Sun Yat-sen UniversityGuangzhou 510080China

Cognitive decline has been linked to periodontitis through an undetermined pathophysiological mechanism.This study aimed to explore the mechanism underlying periodontitis-related cognitive decline and identify therapeutic strategies for this condition.Using single-nucleus RNA sequencing we found that changes in astrocyte number,gene expression,and cell‒cell communication were associated with cognitive decline in mice with periodontitis.In addition,activation of the NOD-like receptor family pyrin domain containing 3(NLRP3)inflammasome was observed to decrease the phagocytic capability of macrophages and reprogram macrophages to a more proinflammatory state in the gingiva,thus aggravating periodontitis.To further investigate this finding,lipid-based nanoparticles carrying NLRP3 siRNA(NPsiNLRP3)were used to inhibit overactivation of the NLRP3 inflammasome in gingival macrophages,restoring the oral microbiome and reducing periodontal inflammation.Furthermore,gingival injection of NPsiNLRP3 reduced the number of Serpina3nhigh astrocytes in the hippocampus and prevented cognitive decline.This study provides a functional basis for the mechanism by which the destruction of periodontal tissues can worsen cognitive decline and identifies nanoparticle-mediated restoration of gingival macrophage function as a novel treatment for periodontitis-related cognitive decline.

关键词： NLRP3 periodontal number

可达性对城市群多模式交通碳排放的空间异质性影响

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交通运输系统工程与信息 2024年第3期24卷 64-74页

作者：马书红陈西芳杨磊赵玉哲曾玉长安大学运输工程学院西安710064

当前,在交通行业碳减排存在巨大挑战以及未来中国城市群交通发展长远规划双重背景下,如何通过改善交通可达性提高居民出行效率和减少碳排放是亟待解决的关键问题之一。本文基于城际出行手机信令数据,从居民出行的角度提出城际多模式交... 详细信息

当前,在交通行业碳减排存在巨大挑战以及未来中国城市群交通发展长远规划双重背景下,如何通过改善交通可达性提高居民出行效率和减少碳排放是亟待解决的关键问题之一。本文基于城际出行手机信令数据,从居民出行的角度提出城际多模式交通客运碳排放量方法,并采用梯度提升决策树(GBDT)模型及多尺度地理加权回归(MGWR)模型探讨可达性对区域碳排放量的空间异质性影响。以关中平原城市群为例进行验证,结果表明:城际公路客运碳排放量远大于铁路,呈现沿交通基础设施线路分布的特征;在整体区域范围内,可达性指标对碳排放水平具有一定的正向边际效应;MGWR能够刻画碳排放与可达性指标关系的空间异质性及尺度差异;经济潜能可达性、介数中心性及接近中心性对城际碳排放具有显著的正向空间异质性影响,但影响尺度不同;公路客运碳排放对介数中心性及接近中心性要素较为敏感,经济潜能对碳排放的影响较为平稳;铁路出行可达性的提升对中心城市的影响效应低于周边区县城市。

关键词：交通工程空间异质性多尺度地理加权回归模型城际交通可达性碳排放

SINAT E3 ligases regulate the stability of the ESCRT component FREE1 in response to iron deficiency in plants

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Journal of Integrative Plant Biology 2020年第9期62卷 1399-1417页

作者： Zhidan Xiao Chao yang Chuanliang Liu Lianming yang shuhong yang Jun Zhou Faqiang Li Liwen Jiang Shi Xiao Caiji Gao Wenjin Shen Guangdong Provincial Key Laboratory of Biotechnology for Plant Development School of Life SciencesSouth China Normal UniversityGuangzhou510631China MOE Key Laboratory of Laser Life Science&Institute of Laser Life Science College of BiophotonicsSouth China Normal UniversityGuangzhou510631China College of Life Sciences South China Agricultural UniversityGuangzhou510642China School of Life Sciences Center for Cell&Developmental Biology and State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongNew TerritoriesHong KongChina State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant ResourcesSchool of Life SciencesSun Yat-sen UniversityGuangzhou510275China

The endosomal sorting complex required for transport (ESCRT) machinery is an ancient, evolutionarily conserved membrane remodeling complex that is es-sential for multivesicular body (MVB) biogenesis in eu-karyotes. FYVE DOMAIN PROTEIN REQUIRED FOR EN-DOSOMAL SORTING 1 (FREE1), which was previously identified as a plant-specific ESCRT component, modu-lates MVB-mediated endosomal sorting and autophagic degradation. Although the basic cellular functions of FREE1 as an ESCRT component have been described, the regulators that control FREE1 turnover remain unknown. Here, we analyzed how FREE1 homeostasis is mediated by the RING-finger E3 ubiquitin ligases, SINA of Arabi-dopsis thaliana (SINATs), in response to iron deficiency. Under iron-deficient growth conditions, SINAT1-4 were induced and ubiquitinated FREE1, thereby promoting its degradation and relieving the repressive effect of FREE1 on iron absorption. By contrast, SINAT5, another SINAT member that lacks ubiquitin ligase activity due to the absence of the RING domain, functions as a protector protein which stabilizes FREE1. Collectively, our findings uncover a hitherto unknown mechanism of homeostatic regulation of FREE1, and demonstrate a unique regu-latory SINAT–FREE1 module that subtly regulates plant response to iron deficiency stress.

关键词： component sorting thereby