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| 1 | Organellar genome assembly methods and comparative analysis of horticultural plants显示文摘Although organellar genomes(including chloroplast and mitochondrial genomes)are smaller than nuclear genomes in size and gene number,organellar genomes are very important for the investigation of plant evolution and molecular ecology mechanisms.Few studies have focused on the organellar genomes of horticultural plants.Approximately 1193 chloroplast genomes and 199 mitochondrial genomes of land plants are available in the National Center for Biotechnology Information(NCBI),of which only 39 are from horticultural plants.In this paper,we report an innovative and efficient method for high-quality horticultural organellar genome assembly from next-generation sequencing(NGS)data.Sequencing reads were first assembled by Newbler,Amos,and Minimus software with default parameters.The remaining gaps were then filled through BLASTN search and PCR.The complete DNA sequence was corrected based on Illumina sequencing data using BWA(Burrows–Wheeler Alignment tool)software.The advantage of this approach is that there is no need to isolate organellar DNA from total DNA during sample preparation.Using this procedure,the complete mitochondrial and chloroplast genomes of an ornamental plant,Salix suchowensis,and a fruit tree,Ziziphus jujuba,were identified.This study shows that horticultural plants have similar mitochondrial and chloroplast sequence organization to other seed plants.Most horticultural plants demonstrate a slight bias toward A+T rich features in the mitochondrial genome.In addition,a phylogenetic analysis of 39 horticultural plants based on 15 protein-coding genes showed that some mitochondrial genes are horizontally transferred from chloroplast DNA.Our study will provide an important reference for organellar genome assembly in other horticultural plants.Furthermore,phylogenetic analysis of the organellar genomes of horticultural plants could accurately clarify the unanticipated relationships among these plants. | Xuelin Wang Feng Cheng Dekai Rohlsen Changwei Bi Chunyan Wang Yiqing Xu Suyun Wei Qiaolin Ye Tongming Yin Ning Ye | 2018 | Horticulture Research2018，5，1： | 4 |
| 2 | Genome-wide identification and characterization of WUSCHEL-related homeobox(WOX) genes in Salix suchowensis显示文摘Members of the WUSCHEL-related homeobox(WOX)transcription factor family are essential for determining cell fate and regulating diverse developmental processes in plants.Many WOX genes have been systematically investigated in woody plants such as Populus trichocarpa,but not in Salix suchowensis.Whole-genome sequence data for S.suchowensis is now available for comprehensive study of WOX genes in S.suchowensis.We thus surveyed the genome of S.suchowensis and demonstrated active expression of 15 WOX genes.In a phylogenetic analysis of WOX genes,the 15 SsWOX genes clustered among the modern/WUS,intermediate and ancient clades similar to the WOX genes of Arabidopsis thaliana.Based on the conserved intron/exon structure,SsWOX genes in the same subgroup had similar conserved exon–intron structures and motif domains.Furthermore,among several SsWOX subgroups,WUS(Wuschel)-box and EAR(the ERF-associated amphiphilic repression)-like motifs were conserved.Expression profiles of WOX genes in roots,stems and leaves indicate that SsWOX genes have various conserved roles in the tissues.Comparative analysis of the expression patterns in Salix suchowensis with that of Arabidopsis suggests that different shoot regeneration abilities are controlled by different WOX genes in plants.The analysis provide an overview of differentially expressed SsWOX genes during shoot regeneration,but also contribute to understanding the evolution of WOX genes in Salicaceae and the interrelations of WOX genes and other transcription factors,providing targets for further study. | Xuelin Wang Changwei Bi Chunyan Wang Qiaolin Ye Tongming Yin Ning Ye | 2019 | Journal of Forestry Research2019，30，5： | 3 |
| 3 | Recursive projection twin support vector machine via within-class vari- ance minimization显示文摘 | CHEN Xiaobo YANG Jian YE Qiaolin | 2011 | Pattern recognition2011，44，1011： | 1 |
| 4 | Least squares twin support vector machine classification via maximum one-class within class variance显示文摘 | Ye Qiaolin Zhao Chunxia Ye Ning | 2012 | Optimization Methods & Software2012，27，1： | 1 |
| 5 | Localized twin svm via convex minimization 显示文摘 | YE Qiaolin ZhAO Chunxia YE Ning | 2011 | Neurocomputing2011，74，4： | 1 |
| 6 | Least squares twin support vector machine classification via maximum one-class within class variance 显示文摘 | Ye Qiaolin Zhao Chunxia Ye Ning | 2012 | Optimization Methods & Software2012，27，1： | 1 |
| 7 | Weighted twin support vector machines with local information andits application显示文摘 | QIAOLIN CHUN XIAZHAO YE SHANGBING GAO | 2012 | Neural Networks2012，，： | 1 |
| 8 | Comparing independent climate-sensitive models of aboveground biomass and diame ter grow th with their compatible simultaneous model system for three larch species in China显示文摘Accurate estimate of tree biomass is essential for forest management.In recent years,several climate-sensitive allometric biomass models with diameter at breast height(D)as a predictor have been proposed for various tree species and climate zones to estimate tree aboveground biomass(AGB).But the allometric models only account for the potential effects of climate on tree biomass and do not simultaneously explain the influence of climate on D growth.In this study,based on the AGB data from 256 destructively sampled trees of three larch species randomly distributed across the five secondary climate zones in northeastern and northern China,we first developed a climate-sensitive AGB base model and a climate-sensitive D growth base model using a nonlinear least square regression separately.A compatible simultaneous model system was then developed with the climate-sensitive AGB and D growth models using a nonlinear seemingly unrelated regression.The potential effects of several temperature and precipitation variables on AGB and D growth were evaluated.The fitting results of climatic sensitive base models were compared against those of their compatible simultaneous model system.It was found that a decreased isothermality([mean of monthly(maximum temperatureminimum temperature)]/(Maximum temperature of the warmest month-Minimum temperature of the coldest month))and total growing season precipitation,and increased annual precipitation significantly increased the values of AGB;an increase of temperature seasonality(a standard deviation of the mean monthly temperature)and precipitation seasonality(a standard deviation of the mean monthly precipitation)could lead to the increase of D.The differences of the model fitting results between the compatible simultaneous system with the consideration of climate effects on both AGB and D growth and its corresponding climate-sensitive AGB and D growth base models were very small and insignificant(p>0.05).Compared to the base models,the inhere nt correlation of AGB with D was taken into account effectively by the proposed compatible model system developed with the climate-sensitive AGB and D grow th models.In addition,the compatible properties of the estimated AGB and D were also addressed substantially in the proposed model system. | Zhigang Gao Qiuyan Wang Zongda Hus Peng Luo Guangshuang Duan Ram PSharma Qiaolin Ye Wenqiang Gao Xinyu Song Liyong Fut | 2019 | International Journal of Biomathematics2019，12，7： | 1 |
| 9 | Weighted twin support vector machines with local information and its application显示文摘 | YE Qiaolin ZHAO Chtmxia GAO Shangbing | 2012 | Neural Networks2012，35，11： | 1 |
| 10 | Least squares twin support vector machine classification via maximum one-class within class variance显示文摘 | Ye Qiaolin Zhao Chunxia Ye Ning | | 0，，01： | 1 |
| 11 | Localized twin svm via convex minimization显示文摘 | YE Qiaolin ZHAO Chunxia YE Ning | 2011 | Neuroeomputing2011，74，4： | 1 |
| 12 | Recursive projection twin support vector machine via within-class variance minimization显示文摘 | CHEN Xiaobo YANG Jian YE Qiaolin | 2011 | Pattern Recognition2011，44，10： | 1 |
| 13 | Localized twin SVM via convex minimization显示文摘 | Ye Qiaolin Zhao Chunxia YeNing | 2011 | Neurocomputing2011，74，4： | 1 |
| 14 | Humanoid Intelligent Display Platform for Audiovisual Interaction and Sound Identification显示文摘This study proposes a rational strategy for the design,fabrication and system integration of the humanoid intelligent display platform(HIDP)to meet the requirements of highly humanized mechanical properties and intelligence for human-machine interfaces.The platform’s sandwich structure comprises a middle lightemitting layer and surface electrodes,which consists of silicon elastomer embedded with phosphor and silk fibroin ionoelastomer,respectively.Both materials are highly stretchable and resilient,endowing the HIDP with skin-like mechanical properties and applicability in various extreme environments and complex mechanical stimulations.Furthermore,by establishing the numerical correlation between the amplitude change of animal sounds and the brightness variation,the HIDP realizes audiovisual interaction and successful identification of animal species with the aid of Internet of Things(IoT)and machine learning techniques.The accuracy of species identification reaches about 100%for 200 rounds of random testing.Additionally,the HIDP can recognize animal species and their corresponding frequencies by analyzing sound characteristics,displaying real-time results with an accuracy of approximately 99%and 93%,respectively.In sum,this study offers a rational route to designing intelligent display devices for audiovisual interaction,which can expedite the application of smart display devices in human-machine interaction,soft robotics,wearable sound-vision system and medical devices for hearing-impaired patients. | Yang Wang Wenli Gao Shuo Yang Qiaolin Chen Chao Ye Hao Wang Qiang Zhang Jing Ren Zhijun Ning Xin Chen Zhengzhong Shao Jian Li Yifan Liu Shengjie Ling | 2023 | Nano-Micro Letters2023，15，12： | 0 |
| 15 | Dynamics and cytokinic regulation of immune cell infiltration in genetically engineered mouse models of pancreatic cancer dictate the sensitivity to immunotherapy显示文摘Dear Editor,Targeting the immune compartment in pancreatic duc-tal adenocarcinoma(PDAC)holds promise for prognostic improvement,yet our knowledge on the spatial and tem-poral dynamics and the molecular modulators of the PDAC-associated immunophenotype is scarce. | Okan Safak Shenghan Wang Carmen Mota Reyes Ibrahim Halil Gürcinar Sergey Tokalov Nedim Can Cevik Kivanc Görgülü Bengi Su Yilmaz Emre Erdogan Linhan Ye Qiaolin Li Elif Arik Sever SamedÖzer Güldal Süyen Helmut Friess Güralp Onur Ceyhan Rouzanna Istvanffy Hana Algül Ihsan Ekin Demir | 2024 | Cancer Communications2024，44，1： | 0 |
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