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| 1 | The HuangZaoSi Maize Genome Provides Insights into Genomic Variation and Improvement History of Maize显示文摘Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of six completed sequeneed maize genomes show that 638 proteins fall into 264 HZS-specific gene families with the majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZSrelated lines reveals the breeding history of HILs. More than 60% of identified selective sweeps were clustered in identity.by.descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. Furthermore, we dem on strated that HZS-specific family genes were not uniformly distributed in the genome but enriched in improvement/function.related genomic regions. This study provides an important and novel resource for maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize. | Chunhui Li Wei Song Yingfeng Luo Shenghan Gao Ruyang Zhang Zi Shi Xiaqing Wang Ronghuan Wang Fengge Wang Jidong Wang Yanxin Zhao Aiguo Su Shuai Wang Xin Li Meijie Luo Shuaishuai Wang Yunxia Zhang Jianrong Ge Xinyu Tan Ye Yuan Xiaochun Bi Hang He Jianbing Yan Yuandong Wang Songnian Hu Jiuran Zhao | 2019 | Molecular Plant2019，12，3： | 15 |
| 2 | Identification of a locus associated with genic male sterility in maize via EMS mutagenesis and bulked-segregant RNA-seq显示文摘Genic male sterility(GMS) is one of the most important resources for exploiting heterosis in crop breeding, so that identifying genomic loci regulating GMS is desirable. However, many regulatory genes controlling GMS have not yet been characterized in maize, owing partly to a lack of genetic materials. We generated a recessive male-sterile maize mutant in the Jing 724 genetic background via ethyl methanesulfonate treatment, and found the male sterility to be due to a single gene mutation. Bulk-segregant RNA sequencing of three replicates indicated that one genomic region located at the end of chromosome 4 was associated with the observed mutant phenotype. Among genes with nonsynonymous mutations,Zm00001 d053895(bHLH51) showed abolished expression in the sterile bulks and was annotated as a bHLH transcription factor orthologous to Arabidopsis AMS, suggesting an association with the male sterility of the mutant. Kompetitive Allele-Specific PCR assays further validated the exclusive correlation of male sterility with the single C-to-T mutation in the fifth exon. The new maize mutant and the potential SNP locus provide novel genetic material for investigating the molecular mechanism underlying tapetal development and may facilitate the improvement of hybrid production systems. | Zi Shi Wen Ren Yanxin Zhao Xiaqing Wang Ruyang Zhang Aiguo Su Shuai Wang Chunhui Li Jiarong Wang Shuaishuai Wang Yunxia Zhang Yulong Ji Wei Song Jiuran Zhao | 2021 | The Crop Journal2021，9，6： | 4 |
| 3 | Comparison of dimension reduction-based logistic regression models for case-control genome-wide association study:principal components analysis vs.partial least squares显示文摘With recent advances in biotechnology, genome-wide association study(GWAS) has been widely used to identify genetic variants that underlie human complex diseases and traits. In case-control GWAS, typical statistical strategy is traditional logistical regression(LR) based on single-locus analysis. However, such a single-locus analysis leads to the well-known multiplicity problem, with a risk of inflating type I error and reducing power. Dimension reduction-based techniques, such as principal component-based logistic regression(PC-LR), partial least squares-based logistic regression(PLS-LR), have recently gained much attention in the analysis of high dimensional genomic data. However, the perfor?mance of these methods is still not clear, especially in GWAS. We conducted simulations and real data application to compare the type I error and power of PC-LR, PLS-LR and LR applicable to GWAS within a defined single nucleotide polymorphism(SNP) set region. We found that PC-LR and PLS can reasonably control type I error under null hypothesis.On contrast, LR, which is corrected by Bonferroni method, was more conserved in all simulation settings. In particular, we found that PC-LR and PLS-LR had comparable power and they both outperformed LR, especially when the causal SNP was in high linkage disequilibrium with genotyped ones and with a small effective size in simulation. Based on SNP set analysis, we applied all three methods to analyze non-small cell lung cancer GWAS data. | Honggang Yi Hongmei Wo Yang Zhao Ruyang Zhang Junchen Dai Guangfu Jin Hongxia Ma Tangchun Wu Zhibin Hu Dongxin Lin Hongbing Shen Feng Chen | 2015 | The Journal of Biomedical Research2015，29，4： | 2 |
| 4 | Global COVID-19 Pandemic Waves: Limited Lessons Learned Worldwide over the Past Year显示文摘The occurrence of coronavirus disease 2019(COVID-19)was followed by a small burst of cases around the world;afterward,due to a series of emergency non-pharmaceutical interventions(NPIs),the increas-ing number of confirmed cases slowed down in many countries.However,the lifting of control measures by the government and the public’s loosening of precautionary behaviors led to a sudden increase in cases,arousing deep concern across the globe.arousing deep concern across the globe.This study evaluates the situation of the COVID-19 pandemic in countries and territories worldwide from January 2020 to February 2021.According to the time-varying reproduction number(R(t))of each country or territory,the results show that almost half of the countries and territories in the world have never controlled the epidemic.Among the countries and territories that had once contained the occurrence,nearly half failed to maintain their prevention and control,causing the COVID-19 pandemic to rebound across the world—resulting in even higher waves in half of the rebounding countries or territories.This work also proposes and uses a time-varying country-level transmission risk score(CTRS),which takes into account both R(t)and daily new cases,to demonstrate country-level or territory-level transmission potential and trends.Time-varying hierarchical clustering of time-varying CTRS values was used to successfully reveal the countries and territories that contributed to the recent aggravation of the global pandemic in the last quarter of 2020 and the beginning of 2021,and to identify countries and territories with an increasing risk of COVID-19 transmission in the near future.Furthermore,a regression analysis indicated that the introduction and relaxation of NPIs,including workplace closure policies and stay-at-home requirements,appear to be associated with recent global transmission changes.In conclu-sion,a systematic evaluation of the global COVID-19 pandemic over the past year indicates that the world is now in an unexpected situation,with limited lessons learned.Summarizing the lessons learned could help in designing effective public responses for constraining future waves of COVID-19 worldwide. | Yongyue Wei Jinxing Guan Xiao Ning Yuelin Li Liangmin Wei Sipeng Shen Ruyang Zhang Yang Zhao Hongbing Shen Feng Chen | 2022 | Engineering2022，8，6： | 1 |
| 5 | Formation of Oxygen Vacancies on the {010} Facets of BiOCl and Visible Light Activity for Degradation of Ciprofloxacin显示文摘 | ZENG Xiaoxing GONG Xiaofeng WAN Yiqun HE Ruyang XU Zhaodi | 2018 | Chemical Research in Chinese Universities2018，34，5： | 1 |
| 6 | Variable selection approach for zero-inflated count data via adaptive lasso显示文摘 | Ping Zeng Yongyue Wei Yang Zhao Jin Liu Liya Liu Ruyang Zhang Jianwei Gou Shuiping Huang Feng Chen | 2014 | Journal of Applied Statistics2014，，4： | 1 |
| 7 | Trash to treasure:lactate and protein lactylation in maize root impacts response to drought显示文摘Lactate,protein lactylation(Kla),and specifically histone lactylation have recently been shown to regulate antipathogenic immune responses in mammals.Herein,after we confirmed the presence and accumulation of lactate in maize roots under drought conditions,a lactylome profiling analysis revealed that Kla modifications were invariably present in maize roots,that there were obvious differences in the lactylomes of drought-sensitive(B73)vs.drought-tolerant(Jing2416)lines,and that growing Jing2416 under drought conditions caused significant decreases in the lactylation of multiple enzymes responsible for fatty acid degradation.Inspired by findings of histone-Kla based epigenetic regulation of immune functions in animals,we initially discovered 37 Kla sites on 16 histones in the maize genome,and again detected obvious differential histone Klamediated trends between two lines by Ch IP-Seq.Notably,only 2.7%of genes with differential histone Kla peaks detected during drought stress were commonly present in both lines,a finding demonstrating that abiotic stress triggers distinct epigenetic activities in diverse germplasm while also strongly supporting that a histone Kla layer of regulation is associated with physiological responses to drought stress.Interestingly,exogenous application of spermidine improved the drought tolerance of B73and substantially altered the levels of lactate,protein lactylation,and histone Kla modification.Thus,beyond extending the known domain of Kla-based biochemical and epigenetic regulation from animal immunity to plant stress physiology,our study suggests the physiological,biochemical,and genetic function of“the best-known metabolic waste”,lactate. | Zi Shi Miaoyi Zhou Wei Song Ya Liu Ronghuan Wang Yuandong Wang Ruyang Zhang Jiuran Zhao Wen Ren | 2023 | Science China(Life Sciences)2023，66，8： | 1 |
| 8 | Assessment of force models on finite-sized particles at finite Reynolds numbers显示文摘Finite-sized inertial spherical particles are fully-resolved with the immersed boundary projection method(IBPM)in the turbulent open-channel flow by direct numerical simulation(DNS).The accuracy of the particle surface force models is investigated in comparison with the total force obtained via the fully-resolved method.The results show that the steady-state resistance only performs well in the streamwise direction,while the fluid acceleration force,the added-mass force,and the shear-induced Saffman lift can effectively compensate for the large-amplitude and high-frequency characteristics of the particle surface forces,especially for the wall-normal and spanwise components.The modified steady-state resistance with the correction effects of the acceleration and the fluid shear can better represent the overall forces imposed on the particles,and it is a preferable choice of the surface force model in the Lagrangian point-particle method. | Ruyang LI Weixi HUANG LihaoZHAO ChunxiaoXU | 2020 | Applied Mathematics and Mechanics(English Edition)2020，41，6： | 1 |
| 9 | Transmission dynamics model and the coronavirus disease 2019 epidemic:applications and challenges显示文摘Since late 2019,the beginning of coronavirus disease 2019(COVID-19)pandemic,transmission dynamics models have achieved great development and were widely used in predicting and policymaking.Here,we provided an introduction to the history of disease transmission,summarized transmission dynamics models into three main types:compartment extension,parameter extension and population-stratified extension models,highlight the key contribution of transmission dynamics models in COVID-19 pandemic:estimating epidemiological parameters,predicting the future trend,evaluating the effectiveness of control measures and exploring different possibilities/scenarios.Finally,we pointed out the limitations and challenges lie ahead of transmission dynamics models. | Jinxing Guan Yang Zhao Yongyue Wei Sipeng Shen Dongfang You Ruyang Zhang Theis Lange Feng Chen | 2022 | Medical Review2022，2，1： | 0 |
| 10 | Statistical analysis for genome-wide association study显示文摘In the past few years, genome-wide association study(GWAS) has made great successes in identifying genetic susceptibility loci underlying many complex diseases and traits. The findings provide important genetic insights into understanding pathogenesis of diseases. In this paper, we present an overview of widely used approaches and strategies for analysis of GWAS, offered a general consideration to deal with GWAS data. The issues regarding data quality control, population structure, association analysis, multiple comparison and visual presentation of GWAS results are discussed; other advanced topics including the issue of missing heritability, meta-analysis, setbased association analysis, copy number variation analysis and GWAS cohort analysis are also briefly introduced. | Ping Zeng Yang Zhao Cheng Qian Liwei Zhang Ruyang Zhang Jianwei Gou Jin Liu Liya Liu Feng Chen | 2015 | The Journal of Biomedical Research2015，29，4： | 0 |
| 11 | Variable Importance Measure System Based on Advanced Random Forest显示文摘The variable importance measure(VIM)can be implemented to rank or select important variables,which can effectively reduce the variable dimension and shorten the computational time.Random forest(RF)is an ensemble learning method by constructing multiple decision trees.In order to improve the prediction accuracy of random forest,advanced random forest is presented by using Kriging models as the models of leaf nodes in all the decision trees.Referring to the Mean Decrease Accuracy(MDA)index based on Out-of-Bag(OOB)data,the single variable,group variables and correlated variables importance measures are proposed to establish a complete VIM system on the basis of advanced random forest.The link of MDA and variance-based sensitivity total index is explored,and then the corresponding relationship of proposed VIM indices and variance-based global sensitivity indices are constructed,which gives a novel way to solve variance-based global sensitivity.Finally,several numerical and engineering examples are given to verify the effectiveness of proposed VIM system and the validity of the established relationship. | Shufang Song Ruyang He Zhaoyin Shi Weiya Zhang | 2021 | Computer Modeling in Engineering & Sciences2021，，7： | 0 |
| 12 | ORF355 confers enhanced salinity stress adaptability to S-type cytoplasmic male sterility maize by modulating the mitochondrial metabolic homeostasis显示文摘Moderate stimuli in mitochondria improve wideranging stress adaptability in animals, but whether mitochondria play similar roles in plants is largely unknown. Here, we report the enhanced stress adaptability of S-type cytoplasmic male sterility(CMS-S) maize and its association with mild expression of sterilizing gene ORF355. A CMS-S maize line exhibited superior growth potential and higher yield than those of the near-isogenic N-type line in saline fields. Moderate expression of ORF355 induced the accumulation of reactive oxygen species and activated the cellular antioxidative defense system. This adaptive response was mediated by elevation of the nicotinamide adenine dinucleotide concentration and associated metabolic homeostasis. Metabolome analysis revealed broad metabolic changes in CMS-S lines, even in the absence of salinity stress. Metabolic products associated with amino acid metabolism and galactose metabolism were substantially changed, which underpinned the alteration of the antioxidative defense system in CMS-S plants. The results reveal the ORF355-mediated superior stress adaptability in CMS-S maize and might provide an important route to developing salt-tolerant maize varieties. | Senlin Xiao Wei Song Jinfeng Xing Aiguo Su Yanxin Zhao Chunhui Li Zi Shi Zhiyong Li Shuai Wang Ruyang Zhang Yuanrong Pei Huabang Chen Jiuran Zhao | 2023 | Journal of Integrative Plant Biology2023，65，3： | 0 |
| 13 | Directing in-situ self-optimization of single-atom catalysts for improved oxygen evolution显示文摘The demand for clean and sustainable energy has encouraged the production of hydrogen from water electrolyzers.To overcome the obstacle to improving the efficiency of water electrolyzers,it is highly desired to fabricate active electrocatalysts for the sluggish oxygen evolution process.However,there is generally an intrinsic gap between the as-prepared and real electrocatalysts due to structure evolution under the oxidative reaction conditions.Here,we combine in-situ anionic leaching and atomic deposition to realize single-atom catalysts with self-optimized structures.The introduced F ions facilitate structural transformation from Co(OH)xF into CoOOH(F),which generates an amorphous edge surface to provide more anchoring sites for Ir single atoms.Meanwhile,the in-situ anionic leaching of F ions elevates the Co valence state of Ir_(1)/CoOOH(F)more significantly than the counterpart without F ions(Ir_(1)/CoOOH),leading to stronger adsorption of oxygenated intermediates.As revealed by electrochemical measurements,the increased Ir loading together with the favored adsorption of*OH intermediates improve the catalytic activity of Ir_(1)/CoOOH(F).Specifically,Ir_(1)/CoOOH(F)delivered a current density of 10 mA cm-2at an overpotential of 238 mV,being lower than 314 mV for Ir_(1)/CoOOH.The results demonstrated the facility of the in-situ optimization process to optimize catalyst structure for improved performance. | Peiyu Ma Chen Feng Huihuang Chen Jiawei Xue Xinlong Ma Heng Cao Dongdi Wang Ming Zuo Ruyang Wang Xilan Ding Shiming Zhou Zhirong Zhang Jie Zeng Jun Bao | 2023 | Journal of Energy Chemistry2023，，5： | 0 |
| 14 | Confinement synergy at the heterointerface for enhanced oxygen evolution显示文摘Two-dimensional transition metal hydroxides with abundant reserves and low prices have played an indispensable role in energy catalytic applications.Recent reports indicated that the incorporation of Fe species into Co-based catalysts can synergistically enhance oxygen evolution reaction(OER)activity.Constructing a heterointerface on the surface of Co-based catalysts can provide a platform to investigate the role of heterointerface in reaction kinetics.Herein,we constructed a Fe-O-Co heterointerface without electronic effect by depositing FeO_(x)clusters on the oxygen vacancies of CoOOH surface.FeO_(x)/CoOOH exhibited excellent OER intrinsic activity,which can deliver the turnover frequency(TOF)of 4.56 s^(-1)at the overpotentials of 300 mV and the Tafel slope of 33 mV·dec^(-1).In-situ electrochemical impedance spectroscopy(EIS)and density functional theory(DFT)calculations demonstrated that the synergistic effect between Fe sites and Co sites confined at the Fe-O-Co heterointerface accelerated the charge transfer during OER and optimized the adsorption of oxygen intermediates,consequently enhancing OER. | Dongdi Wang Shanshan Ruan Peiyu Ma Ruyang Wang Xilan Ding Ming Zuo Lidong Zhang Zhirong Zhang Jie Zeng Jun Bao | 2023 | Nano Research2023，16，7： | 0 |
| 15 | Nursing Effect of Pulmonary Rehabilitation in Patients with Chronic Obstructive Pulmonary Disease显示文摘Objective:To study the effect of pulmonary rehabilitation nursing in nursing of patients with chronic obstructive pulmonary disease(COPD).Methods:30 cases of experimental subjects,diagnosed with COPD,were included in the observation group with pulmonary rehabilitation nursing,while the control group received routine nursing,and the data between the groups were compared.Results:After nursing,the observation group showed significantly improved lung function,higher nursing satisfaction,6-minute walking test(6WMT),World Health Organization Quality of Life(WHOQOL-BREF)score,and self-care ability score,compared to the control group,with P<0.05,indicating a statistical difference.Conclusion:Pulmonary rehabilitation nursing is applied in the nursing of COPD patients with ideal effect. | Qi Cheng Fei Lai Ruyang Song Liu Yang Shuang Long | 2022 | Journal of Clinical and Nursing Research2022，6，6： | 0 |
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