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| 1 | Sequencing of Cultivated Peanut, Arachis hypogaea, Yields Insights into Genome Evolution and Oil Improvement显示文摘Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut. | Xiaoping Chen Qing Lu Hao Liu Jianan Zhang Yanbin Hong Haofa Lan Haifen Li Jinpeng Wang Haiyan Liu Shaoxiong Li Manish K.Pandey Zhikang Zhang Guiyuan Zhou Jigao Yu Guoqiang Zhang Jiaqing Yuan Xingyu Li Shijie Wen Fanbo Meng Shanlin Yu Xiyin Wang Kadambot H.M.Siddique Zhong-Jian Liu Andrew H.Paterson Rajeev K.Varshney Xuanqiang Liang | 2019 | Molecular Plant2019，12，7： | 23 |
| 2 | Genome Alignment Spanning Major Poaceae Lineages Reveals Heterogeneous Evolutionary Rates and Alters Inferred Dates for KeyEvolutionary Events显示文摘 | Xiyin Wa ng Jingpeng Wang Dianchuan Jin Hui Guo Tae-Ho Lee Tao Liu Andrew H. Paterson | 2015 | Molecular Plant2015，8，6： | 18 |
| 3 | Efficacy of Banxia Xiexin decoction in a rat model of chronic atrophic gastritis显示文摘OBJECTIVE:To investigate the effectiveness of Banxia Xiexin decoction(BXD)in a rat model of chronic atrophic gastritis(CAG).METHODS:Sixty 6-week-old healthy Wistar rats(30 males,30 females)were used in the present study.A rat model of CAG was successfully established using the combined active immunization/ethanol/sodium deoxycholate method.BXD was prepared from a mixture of seven Chinese herbs,and was intragastrically administered to CAG rats at three different doses(6,12,and 24 g·kg^-1·d^-1).Af-ter 24 weeks,the rats were euthanized,and gastric tissue specimens were collected.Gastric mucosal specimens were stained with hematoxylin and eosin for histological examination to evaluate the degree of inflammation and morphological changes.Immunohistochemical staining was performed to examine the mucosal expression of proliferating cell nuclear antigen.Serum gastrin levels were measured using radioimmunoassay.The expression of Notch signaling-associated genes was examined by quantitative polymerase chain reaction and Western blot assay.RESULTS:BXD at all three doses significantly reversed the adverse effects generated by CAG in rats.Compared with control rats,the CAG rats who were administered BXD had an accelerated growth rate,reduced inflammatory cell infiltration,improved gastric mucosal morphology,augmented thickness of the gastric mucosa,increased number of gastric glands,enhanced mucosal expression of proliferating cell nuclear antigen,and elevated serum gastrin levels. | Bai Yu Chen Yongcan Chen Yu Yan Maoxiang Wei Hongquan Wang Hengcang Zeng Guoliang Yang Xiyin | 2019 | Journal of Traditional Chinese Medicine2019，39，6： | 14 |
| 4 | Discovery of a male-biased mutant family and identification of a male-specific SCAR marker in gynogenetic gibel carp Carassius auratus gibelio显示文摘Gibel 鲤鱼(Carassius auratus gibelio ) 是一特别地有在自然产地的男性的次要的比率的 gynogenetic 种类,而是它的男起源和性决心机制是未知的。在这研究,一个偏导男性的变异的家庭从 gynogenetic gibel 鲤鱼被发现,并且一个男性特定的疤标记从变异的家庭被识别。正常精子发生被免疫荧光组织化学在男睾丸观察。将近相同的 AFLP 侧面在男性和女性之间被观察,但是一男性特定 86 bp AFLP 碎片被性水池 bulked segregant 分析并且单个屏蔽屏蔽。基于男性特定的 AFLP 碎片, 579 个 bp 序列的一个总数被染色体走克隆。随后,一个男性特定的疤标记被设计,并且男性特定的 DNA 碎片被证实稳定地被传给下一代并且一致地仅仅在男性检测了。 | Da Wang Huiling Mao Jinxia Peng Xiyin Li Li Zhou Jianfang Gui | 2009 | Progress in Natural Science:Materials International2009，19，11： | 11 |
| 5 | PhaseⅠ/Ⅱtrial evaluating concurrent carbon-ion radiotherapy plus chemotherapy for salvage treatment of locally recurrent nasopharyngeal carcinoma显示文摘Background: After deinitive chemoradiotherapy for non-metastatic nasopharyngeal carcinoma(NPC), more than 10% of patients will experience a local recurrence. Salvage treatments present signiicant challenges for locally recurrent NPC. Surgery, stereotactic ablative body radiotherapy, and brachytherapy have been used to treat locally recurrent NPC. However, only patients with small-volume tumors can beneit from these treatments. Re-irradiation with X-ray—based intensity-modulated radiotherapy(IMXT) has been more widely used for salvage treatment of locally recurrent NPC with a large tumor burden, but over-irradiation to the surrounding normal tissues has been shown to cause frequent and severe toxicities. Furthermore, locally recurrent NPC represents a clinical entity that is more radioresistant than its primary counterpart. Due to the inherent physical advantages of heavy-particle therapy, precise dose delivery to the target volume(s), without exposing the surrounding organs at risk to extra doses, is highly feasible with carbon-ion radiotherapy(CIRT). In addition, CIRT is a high linear energy transfer(LET) radiation and provides an increased relative biological efectiveness compared with photon and proton radiotherapy. Our prior work showed that CIRT alone to 57.5 Gy E(gray equivalent), at 2.5 Gy E per daily fraction, was well tolerated in patients who were previously treated for NPC with a deinitive dose of IMXT. The short-term response rates at 3–6 months were also acceptable. However, no patients were treated with concurrent chemotherapy. Whether the addition of concurrent chemotherapy to CIRT can beneit locally recurrent NPC patients over CIRT alone has never been addressed. It is possible that the beneits of high-LET CIRT may make radiosensitizing chemotherapy unnecessary. We therefore implemented a phase I/II clinical trial to address these questions and present our methodology and results.Methods and design: The maximal tolerated dose(MTD) of re-treatment using raster-scanning CIRT plus concurrent cisplatin will be determined in the phase I, dose-escalating stage of this study. CIRT dose escalation from 52.5 to 65 Gy E(2.5 Gy E × 21–26 fractions) will be delivered, with the primary endpoints being acute and subacute toxicities. Eicacy in terms of overall survival(OS) and local progression-free survival of patients after concurrent chemotherapy plus CIRT at the determined MTD will then be studied in the phase II stage of the trial. We hypothesize that CIRT plus chemotherapy can improve the 2-year OS rate from the historical 50% to at least 70%.Conclusions: Re-treatment of locally recurrent NPC using photon radiation techniques, including IMXT, provides moderate eicacy but causes potentially severe toxicities. Improved outcomes in terms of eicacy and toxicity proile are expected with CIRT plus chemotherapy. However, the MTD of CIRT used concurrently with cisplatin-based chemotherapy for locally recurrent NPC remains to be determined. In addition, whether the addition of chemotherapy to CIRT is needed remains unknown. These questions will be evaluated in the dose-escalating phase I and randomized phase II trials. | Lin Kong Jing Gao Jiyi Hu Weixu Hu Xiyin Guan Rong Lu Jiade J.Lu | 2016 | Chinese Journal of Cancer2016，35，12： | 8 |
| 6 | Concurrent chemoradiotherapy comparison of taxanes and platinum versus 5-fluorouracil and platinum in nasopharyngeal carcinoma treatment显示文摘 | Chen Xichuang Hong Yuan Feng Jinhua Ye Jianlin Zheng Panpan Guan Xiyin You Xiaohong Song Huizhu | 2014 | Chinese Medical Journal2014，，1： | 8 |
| 7 | The structure of weak Pareto solution sets in piecewise linear multiobjective optimization in normed spaces显示文摘In general normed spaces,we consider a multiobjective piecewise linear optimization problem with the ordering cone being convex and having a nonempty interior.We establish that the weak Pareto optimal solution set of such a problem is the union of finitely many polyhedra and that this set is also arcwise connected under the cone convexity assumption of the objective function.Moreover,we provide necessary and suffcient conditions about the existence of weak(sharp) Pareto solutions. | ZHENG XiYin YANG XiaoQi | 2008 | Science China Mathematics2008，51，7： | 6 |
| 8 | WGDI:A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes显示文摘Evidence of whole-genome duplications(WGDs)and subsequent karyotype changes has been detected in most major lineages of living organisms on Earth.To clarify the complex resulting multi-layered patterns of gene collinearity in genome analyses,there is a need for convenient and accurate toolkits.To meet this need,we developed WGDI(Whole-Genome Duplication Integrated analysis),a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidization events and cross-species genome alignments.WGDI supports three main workflows(polyploid inference,hierarchical inference of genomic homology,and ancestral chromosome karyotyping)that can improve the detection of WGD and characterization of WGD-related events based on high-quality chromosome-level genomes.Significantly,it can extract complete synteny blocks and facilitate reconstruction of detailed karyotype evolution.This toolkit is freely available at GitHub(https://github.com/SunPengChuan/wgdi).As an example of its application,WGDI convincingly clarified karyotype evolution in Aquilegia coerulea and Vitis vinifera following WGDs and rejected the hypothesis that Aquilegia contributed as a parental lineage to the allopolyploid origin of core dicots. | Pengchuan Sun Beibei Jiao Yongzhi Yang Lanxing Shan Ting Li Xiaonan Li Zhenxiang Xi Xiyin Wang Jianquan Liu | 2022 | Molecular Plant2022，15，12： | 5 |
| 9 | Coriander Genomics Database:a genomic,transcriptomic,and metabolic database for coriander显示文摘Coriander(Coriandrum sativum L.),also known as cilantro,is a globally important vegetable and spice crop.Its genome and that of carrot are models for studying the evolution of the Apiaceae family.Here,we developed the Coriander Genomics Database(CGDB,http://cgdb.bio2db.com/)to collect,store,and integrate the genomic,transcriptomic,metabolic,functional annotation,and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related plants.Using these data sets in the CGDB,we intriguingly found that seven transcription factor(TF)families showed significantly greater numbers of members in the coriander genome than in the carrot genome.The highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15,followed by those for tubby protein(TUB)and heat shock factors.As a demonstration of CGDB applications,we identified 17 TUB family genes and conducted systematic comparative and evolutionary analyses.RNA-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in coriander.CGDB allows bulk downloading,significance searches,genome browser analyses,and BLAST searches for comparisons between coriander and other plants regarding genomics,gene families,gene collinearity,gene expression,and the metabolome.A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific questions.CGDB will be continuously updated,and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants. | Xiaoming Song Fulei Nie Wei Chen Xiao Ma Ke Gong Qihang Yang Jinpeng Wang Nan Li Pengchuan Sun Qiaoying Pei Tong Yu Jingjing Hu Xinyu Li Tong Wu Shuyan Feng Xiu-Qing Li Xiyin Wang | 2020 | Horticulture Research2020，7，1： | 4 |
| 10 | A state-of-the-art review of asphalt pavement surface texture and its measurement techniques显示文摘To understand the research status of asphalt pavement texture,the related achievements and progress of pavement surface texture were systematically sorted out from three aspects:the characterization of pavement surface texture,the texture measurement and evaluation,and the relationship between texture and the skid resistance.Based on the statistical geometric characteristics,the spectral characteristics,the fractal characteristics and the multifractal characteristics,the characteristics of pavement texture were discussed.The test methods of pavement texture were divided into two categories:direct measurement methods and indirect measurement methods.The advantages and disadvantages of each measurement method were summarized.The effects of macro-texture and micro-texture on asphalt pavement were discussed,respectively.The relationship between texture and skid resistance was studied.This review shows that multifractal theory should be further studied from the aspect of road engineering.High-precision non-contact integrated detection technology should be further studied to meet the needs of complex testing environments.The method of finite element numerical simulation has potential for the analysis of pavement skid resistance.In addition,methods such as big data analysis,neural network,and deep learning should be studied to achieve the intelligent perception and management of the whole state of skid resistance prediction. | Siyu Chen Xiyin Liu Haoyuan Luo Jiangmiao Yu Fuda Chen Yang Zhang Tao Ma Xiaoming Huang | 2022 | Journal of Road Engineering2022，2，2： | 3 |
| 11 | Survey of spinal cord injury-induced neurogenic bladder studies using the Web of Science显示文摘OBJECTIVE:To identify global trends in research on spinal cord injury-induced neurogenic bladder, through a bibliometric analysis using the Web of Science. DATA RETRIEVAL:We performed a bibliometric analysis of studies on spinal cord injury-induced neurogenic bladder using the Web of Science.Data retrieval was performed using key words'spinal cord injury','spinal injury','neurogenic bladder','neuropathic bladder','neurogenic lower urinary tract dysfunction','neurogenic voiding dysfunction','neurogenic urination disorder'and 'neurogenic vesicourethral dysfunction'. SELECTION CRITERIA:Inclusion criteria:(a)published peer-reviewed articles on spinal cord injury-induced neurogenic bladder indexed in the Web of Science;(b)type of articles:original research articles and reviews;(c)year of publication:no limitation.Exclusion criteria:(a)articles that required manual searching or telephone access;(b)Corrected papers and book chapters. MAIN OUTCOME MEASURES:(1)Annual publication output;(2)distribution according to journals; (3)distribution according to subject areas;(4)distribution according to country;(5)distribution according to institution;and(6)top cited publications. RESULTS:There were 646 research articles addressing spinal cord injury-induced neurogenic bladder in the Web of Science.Research on spinal cord injury-induced neurogenic bladder was found in the Science Citation Index-Expanded as of 1946.The United States,Ireland and Switzerland were the three major countries contributing to studies in spinal cord injury-induced neurogenic bladder in the 1970s.However,in the 1990s,the United States,the United Kingdom,the Netherlands,Germany and Japan published more papers on spinal cord injury-induced neurogenic bladder than Switzerland,and Ireland fell off the top ten countries list.In this century,the United States ranks first in spinal cord injury-induced neurogenic bladder studies,followed by France,the United Kingdom,Germany,Switzerland and Japan.Subject categories including urology, nephrology and clinical neurology,as well as rehabilitation,are represented in spinal cord injury-induced neurogenic bladder studies. CONCLUSION:From our analysis of the literature and research trends,we conclude that spinal cord injury-induced neurogenic bladder is a hot topic that will continue to generate considerable research interest in the future. | Benjing Zou Yongli Zhang Yucheng Li Zantao Wang Ping Zhang Xiyin Zhang Bingdong Wang Zhixin Long Feng Wang Guo Song Yan Wang | 2012 | Neural Regeneration Research2012，7，23： | 3 |
| 12 | Epithelial-Mesenchymal Transitions and the Expression of Twist in MCF-7/ADR, Human Multidrug-Resistant Breast Cancer Cells显示文摘0BJECTIVE To study the expression levels of Twist and epithelialmesenchymal transitions in multidrug-resistant MCF-7/ADR breast cancer cells, and to study the relationship between multidrug resistance (MDR) and metastatic potential of the cells. METHODS RT-PCR, immunohistochemical and Western blotting methods were used to examine the changes of expression levels of the transcription factor Twist, E-cadherin and N-cadherin in the MCF-7 breast cancer cell line and its multidrug-resistant variant, MCF-7/ADR. RESULTS In MCF-7 cells, the expression of E-cadherin can be detected, but there is no expression of Twist or N-cadherin. In MCF-7/ADR cells, E-cadherin expression is lost, but the expression of two other genes was significantly positive. CONCLUSION Epithelial-mesenchymal transitions induced by Twist, may have a relationship with enhanced invasion and metastatic potential during the development of multidrug-resistant MCF-7/ADR breast cancer cells. | Fei Zhang Yurong Shi Lin Zhang Bin Zhang Xiyin Wei Yi Yang Rui Wang Ruifang Niu | 2007 | Chinese Journal of Clinical Oncology2007，4，1： | 2 |
| 13 | Optimal control problem in an epidemic disease SIS model with stages and delays显示文摘 | Yongzhen Pei Miaomiao Chen Xiyin Liang Zhumei Xia Yunfei Lv Changguo Li | 2016 | International Journal of Biomathematics2016，9，5： | 2 |
| 14 | An approach for detecting LDoS attack based on cloud model显示文摘Cybersecurity has always been the focus of Internet research.An LDoS attack is an intelligent type of DoS attack,which reduces the quality of network service by periodically sending high-speed but short-pulse attack traffic.Because of its concealment and low average rate,the traditional DoS attack detection methods are challenging to be effective.The existing LDoS attack detection methods generally have the problems of high FPR and FNR.A cloud model-based LDoS attack detection method is proposed,and a classifier based on SVM is used to train and classify the feature parameters.The detection method is verified and tested in the NS2 simulation platform and Test-bed network environment.Compared with the existing research results,the proposed method requires fewer samples,and it has lower FPR and FNR. | Wei SHI Dan TANG Sijia ZHAN Zheng QIN Xiyin WANG | 2022 | Frontiers of Computer Science2022，16，6： | 1 |
| 15 | Integrated network analyses identify MYB4R1 neofunctionalization in the UV-B adaptation of Tartary buckwheat显示文摘A hallmark of adaptive evolution is innovation in gene function,which is associated with the development of distinct roles for genes during plant evolution;however,assessing functional innovation over long periods of time is not trivial.Tartary buckwheat(Fagopyrum tataricum)originated in the Himalayan region and has been exposed to intense UV-B radiation for a long time,making it an ideal species for studying novel UV-B response mechanisms in plants.Here,we developed a workflow to obtain a co-functional network of UV-B responses using data from more than 10,000 samples in more than 80 projects with multi-species and multiomics data.Dissecting the entire network revealed that flavonoid biosynthesis was most significantly related to the UV-B response.Importantly,we found that the regulatory factor MYB4R1,which resides at the core of the network,has undergone neofunctionalization.In vitro and in vivo experiments demonstrated that MYB4R1 regulates flavonoid and anthocyanin accumulation in response to UV-B in buckwheat by binding to L-box motifs in the FtCHS,FtFLS,and FtUFGT promoters.We used deep learning to develop a visual discrimination model of buckwheat flavonoid content based on natural populations exposed to global UV-B radiation.Our study highlights the critical role of gene neofunctionalization in UV-B adaptation. | Moyang Liu Wenjun Sun Zhaotang Ma Chaocheng Guo Jiahao Chen Qi Wu Xiyin Wang Hui Chen | 2022 | Plant Communications2022，3，6： | 1 |
| 16 | Virtual differential GPS based on SBAS signal显示文摘 | Xiyin Li | 2004 | GPS Solutions2004，7，8： | 1 |
| 17 | Adaptive synchronization for generalized Lorenz systems显示文摘 | LIANG Xiyin ZHANG Jiangfeng XIA Xiaohua | 2008 | IEEE Trans on Automatic Control2008，53，7： | 1 |
| 18 | Mitochondrial metabolism transition cooperates with nuclear reprogramming during induced pluripotent stem cell generation显示文摘 | Wenbo Liu Qi Long Keshi Chen Shengbiao Li Ge Xiang Shen Chen Xiyin Liu Yuxing Li Liang Yang Delu Dong Cheng Jiang Zhenhua Feng Dajiang Qin Xingguo Liu | 2013 | Biochemical and Biophysical Research Communications2013，，： | 1 |
| 19 | Effects of recombinant human endostatin and its synergy with cisplatin on circulating endothelial cells and tumor vascular normalization in A549 xenograft murine model显示文摘 | Na Li Dawei Zheng Xiyin Wei Ziliang Jin Cuicui Zhang Kai Li | 2012 | Journal of Cancer Research and Clinical Oncology2012，，7： | 1 |
| 20 | Linear regularity for a collection of subsmooth sets in Banach spaces显示文摘 | ZHENG Xiyin Ng K F | 2008 | SIAM J ODtim2008，19，： | 1 |
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