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| 1 | A new approach to dissecting complex traits by combining quantitative trait transcript (QTT) mapping and diallel cross analysis显示文摘A promising way to uncover the genetic architectures underlying complex traits may lie in the ability to recognize the genetic variants and expression transcripts that are responsible for the traits' inheritance.However,statistical methods capable of investigating the association between the inheritance of a quantitative trait and expression transcripts are still limited.In this study,we described a two-step approach that we developed to evaluate the contribution of expression transcripts to the inheritance of a complex trait.First,a mixed linear model approach was applied to detect significant trait-associated differentially expressed transcripts.Then,conditional analysis were used to predict the contribution of the differentially expressed genes to a target trait.Diallel cross data of cotton was used to test the application of the approach.We proposed that the detected differentially expressed transcripts with a strong impact on the target trait could be used as intermediates for screening lines to improve the traits in plant and animal breeding programs.It can benefit the discovery of the genetic mechanisms underlying complex traits. | YANG DaiGang YE ChengYin MA XiongFeng ZHU ZhiHong ZHOU XiaoJian WANG HaiFeng MENG QingQin PEI XiaoYu YU ShuXun ZHU Jun | 2012 | Chinese Science Bulletin2012，57，21： | 3 |
| 2 | Statistical Fluctuation Analysis for Measurement-Device- Independent Quantum Key Distribution显示文摘 | MA Xiongfeng FUNG C F RAZAVI M | 2012 | Physical Review A2012，86，05： | 1 |
| 3 | Grey correlational and SSR analyses of cotton hybrids显示文摘Ten upland cotton strains exhibiting 3 fiber quality traits and 8 yield traits,were grown for two years in an investigation of the correlation between grey relational analysis(GRA) and genetic identity in heterosis of cotton hybrid. The aim was to establish the optimal approach for heterosis prediction and parent selection. Plant traits data were collected and analyzed for GRA. In addition,72 simple sequence repeat(SSR) markers were examined and 148 polymorphisms were detected. Correlation analysis of GRA,genetic identity,F1 fiber quality and yield heterosis was conducted. Significant differences were observed between the two analytic methods,whereas comparable predictions were given for yield heterosis. GRA for yield exhibited slightly higher correlation than genetic identity analysis,with a correlation coefficient of 0.49. GRA and genetic analysis exhibited overlapping yet distinct advantages in heterosis prediction. Therefore,these analytical methods should be integrated to achieve the optimal heterosis prediction and parent selection. | Ma Xiongfeng Yang Daigang Zhou Xiaojian Zhang Xianliang Guo Ruilin Wang Haifeng Meng Qingqin Pei Xiaoyu Zhou Kehai Zhang Wensheng | 2013 | Engineering Sciences2013，11，5： | 1 |
| 4 | Experimental exploration of five-qubit quantum error-correcting code with superconducting qubits显示文摘Quantum error correction is an essential ingredient for universal quantum computing.D espite tremendous experimental efforts in the study of quantum error correction,to date,there has been no demonstration in the realis ation of universal quantum error-correcting code,with the subsequent verification of all key features including the identification of an arbitrary physical error,the capability for transversal manipulation of the logical state and state decoding.To address this challenge,we experimentally realise the [5,1,3]code,the so-called smallest perfect code that permits corrections of generic single-qubit errors.In the experiment,having optimised the encoding circuit,we employ an array of superconducting qubits to realise the [5,1,3] code for several typical logical states including the magic state,an indispensable resource for realising non-Clifford gates.The encoded states are prepared with an average fidelity of 57.1(3)% while with a high fidelity of 98.6(1)% in the code space.Then,the arbitrary single-qubit errors introduced manually are identified by measuring the stabilisers.We further implement logical Pauli operations with a fidelity of 97.2(2)% within the code space.Finally,we realise the decoding circuit and recover the input state with an overall fidelity of 74.5(6)%,in total with 92 gates.Our work demonstrates each key aspect of the [5,1,3] code and verifies the viability of experimental realisation of quantum error-correcting codes with superconducting qubits. | Ming Gong Xiao Yuan Shiyu Wang Yulin Wu Youwei Zhao Chen Zha Shaowei Li Zhen Zhang Qi Zhao Yunchao Liu Futian Liang Jin Lin Yu Xu Hui Deng Hao Rong He Lu Simon C.Benjamin Cheng-Zhi Peng Xiongfeng Ma Yu-Ao Chen Xiaobo Zhu Jian-Wei Pan | 2022 | National Science Review2022，9，1： | 1 |
| 5 | Decoy State Quantum Key Distribution显示文摘 | LO H K MA Xiongfeng CHEN Kang | 2005 | Physical Re-view Letters2005，94，23： | 1 |
| 6 | Decoy-State Protocol for Quantum Cryptography with Four Different Intensities of Coherent Light显示文摘 | LO H K MA Xiongfeng CHEN Kai | 2005 | Phys- ical Review Letters2005，94，23： | 1 |
| 7 | Scalable fast benchmarking for individual quantum gates with local twirling显示文摘With the development of controllable quantum systems,fast and practical characterization of multi-qubit gates has become essential for building high-fidelity quantum computing devices.The usual way to fulfill this requirement via randomized benchmarking demands complicated implementation of numerous multi-qubit twirling gates.How to efficiently and reliably estimate the fidelity of a quantum process remains an open problem.This work thus proposes a character-cycle benchmarking protocol and a character-average benchmarking protocol using only local twirling gates to estimate the process fidelity of an individual multi-qubit operation.Our protocols were able to characterize a large class of quantum gates including and beyond the Clifford group via the local gauge transformation,which forms a universal gate set for quantum computing.We demonstrated numerically our protocols for a non-Clifford gate—controlled-(T X)and a Clifford gate—five-qubit quantum errorcorrecting encoding circuit.The numerical results show that our protocols can efficiently and reliably characterize the gate process fidelities.Compared with the cross-entropy benchmarking,the simulation results show that the character-average benchmarking achieves three orders of magnitude improvements in terms of sampling complexity. | YIHONG ZHANG WENJUN YU PEI ZENG GUODING LIU XIONGFENG MA | 2023 | Photonics Research2023，11，1： | 0 |
| 8 | Patterns of presence-absence variants in Upland cotton显示文摘Dear Editor,Sources of genetic variations in genomes include small-scale sources(such as single-nucleotide polymorphisms(SNPs),insertions/deletions(InDels),and simple sequence repeats and larger-scale structural variations(mainly presence-absence variants(PAVs))and copy number variants).PAVs are sequences that are either inserted or missing in genomes in comparison with a reference sequence or genome.PAVs can have a much longer sequence than SNPs and InDels,as illustrated in the human genome(Conrad et al.,2010).PAVs are important genomic structural variations that can directly affect genomic structure and key functional genes in the genome(Kumar et al.,2007).Moreover,the use of PAVs for studying quantitative traits has been valuable(Lam et al.,2010). | Junfang Liu Xianliang Zhang Lingling Dou Wei Li Xiaojian Zhou Yangai Liu Xiaoyu Pei Zhongying Ren Wensheng Zhang Huaizhu Li Wenbo Wang Changsong Zou Kunlun He Fei Zhang Wenyu Ma Haihong Shang Hongbin Li Daigang Yang Guanghui Xiao Xiongfeng Ma | 2020 | Science China(Life Sciences)2020，63，10： | 0 |
| 9 | CIDP: a multi-functional platform for designing CRISPR sgRNAs显示文摘Dear Editor,Compared with traditional technologies affecting gene expression,changing DNA sequences of target genes is one of the most outstanding characters of CRISPR(Clustered Regularly Interspaced Short Palindromic Repeats).Single-guide RNAs(sgRNAs)guiding endonuclease Cas to target sites is a crucial step of CRISPR-Cas system for changing DNA sequences.An ideal sgRNA should only bind to the target gene.However,similar sequences of non-target sites can also be recognized leading to off-target effects[1]. | Dong Xu Jin Zhang Xianjia Zhao Yuze Hou Heling Jiang Wenchuang He Xiongfeng Ma Weihua Pan | 2023 | Horticulture Research2023，10，7： | 0 |
| 10 | Rigid ureteroscopy, a neglected choice for stent removal: a randomized controlled trial to compare rigid ureteroscopy, flexible cystoscopy, and rigid cystoscopy显示文摘To the Editor:As one of the most powerful tools for urologists,ureteral stents are often used in diseases such as calculi,obstruction,ureteral injury,and kidney transplantation and are removed after 3 days to 4 weeks with a visualization instrument.Initially,rigid cystoscopy(RC)was most often used for stent removal,but due to its inflexibility and large diameter,RC often results in pain and potential damage to patients like hematuria,pain,and lower urinary tract symptoms,especially to men. | Boya Li Xiongfeng Zeng Deyi Luo Yucheng Ma Hong Li Kunjie Wang | 2022 | Chinese Medical Journal2022，135，22： | 0 |
| 11 | Genomic divergence in cotton germplasm related to maturity and heterosis显示文摘Commercial varieties of upland cotton(Gossypium hirsutum)have undergone extensive breeding for agronomic traits,such as fiber quality,disease resistance,and yield.Cotton breeding programs have widely used Chinese upland cotton source germplasm(CUCSG)with excellent agronomic traits.A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles.Here,we analyzed 10,522 high-quality singlenucleotide polymorphisms(SNP)with the CottonSNP63 K microarray in 137 cotton accessions(including 12 hybrids of upland cotton).These data were used to investigate the genetic diversity,population structure,and genomic characteristics of each population and the contribution of these loci to heterosis.Three subgroups were identified,in agreement with their knownpedigrees,geographical distributions,and times since introduction.For each group,we identified lineagespecific genomic divergence regions,which potentially harbor key alleles that determine the characteristics of each group,such as early maturity-related loci.Investigation of the distribution of heterozygous loci,among 12 commercial cotton hybrids,revealed a potential role for these regions in heterosis.Our study provides insight into the population structure of upland cotton germplasm.Furthermore,the overlap between lineagespecific regions and heterozygous loci,in the high-yield hybrids,suggests a role for these regions in cotton heterosis. | Shoupu He Gaofei Sun Longyu Huang Daigang Yang Panhong Dai Dayun Zhou Yuzhen Wu Xiongfeng Ma Xiongming Du Shoujun Wei Jun Peng Meng Kuang | 2019 | Journal of Integrative Plant Biology2019，61，8： | 0 |
| 12 | GhAP1-D3 positively regulates flowering time and early maturity with no yield and fiber quality penalties in upland cotton显示文摘Flowering time(FTi)is a major factor determining how quickly cotton plants reach maturity.Early maturity greatly affects lint yield and fiber quality and is crucial for mechanical harvesting of cotton in northwestern China.Yet,few quantitative trait loci(QTLs)or genes regulating early maturity have been reported in cotton,and the underlying regulatory mechanisms are largely unknown.In this study,we characterized 152,68,and 101 loci that were significantly associated with the three key early maturity traits—FTi,flower and boll period(FBP)and whole growth period(WGP),respectively,via four genome-wide association study methods in upland cotton(Gossypium hirsutum).We focused on one major early maturity-related genomic region containing three single nucleotide polymorphisms on chromosome D03,and determined that GhAP1-D3,a gene homologous to Arabidopsis thaliana APETALA1(AP1),is the causal locus in this region.Transgenic plants overexpressing GhAP1-D3 showed significantly early flowering and early maturity without penalties for yield and fiber quality compared to wild-type(WT)plants.By contrast,the mutant lines of GhAP1-D3 generated by genome editing displayed markedly later flowering than the WT.GhAP1-D3 interacted with GhSOC1(SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1),a pivotal regulator of FTi,both in vitro and in vivo.Changes in GhAP1-D3 transcript levels clearly affected the expression of multiple key flowering regulatory genes.Additionally,DNA hypomethylation and high levels of H3K9ac affected strong expression of GhAP1-D3 in early-maturing cotton cultivars.We propose that epigenetic modifications modulate GhAP1-D3 expression to positively regulate FTi in cotton through interaction of the encoded GhAP1 with GhSOC1 and affecting the transcription of multiple flowering-related genes.These findings may also lay a foundation for breeding early-maturing cotton varieties in the future. | Caixiang Wang Juanjuan Liu Xiaoyu Xie Ji Wang Qi Ma Pengyun Chen Delong Yang Xiongfeng Ma Fushun Hao Junji Su | 2023 | Journal of Integrative Plant Biology2023，65，4： | 0 |
| 13 | Solution-processed quantum-dot light-emitting diodes combining ultrahigh operational stability,shelf stability,and luminance显示文摘The shelf-stability issue,originating from the ZnO-induced positive aging effect,poses a significant challenge to industrializing the display technology based on solution-processed quantum-dot light-emitting diodes(QLEDs).Currently,none of the proposed solutions can simultaneously inhibit exciton quenching caused by the ZnO-based electron-transporting layer(ETL)and retain other advantages of ZnO.Here in this work,we propose a bilayer design of ETL in which a buffer layer assembled of SnO_(2) nanoparticles(NPs)suppresses the QD-ETL exciton quenching and tunes charge balance while ZnO NPs provide high electron conductivity.As a result,the bottom-emitting QLED combining capped ZnO and SnO_(2) buffer exhibit a maximum luminance over 100,000 cd m^(−2) and a T95 operational lifetime averaging 6200 h at 1000 cd m^(−2) on the premise of entirely inhibiting positive aging. | Zi Ye Mengyu Chen Xingtong Chen Wenchen Ma Xiaojuan Sun Longjia Wu Xiongfeng Lin Yu Chen Song Chen | 2022 | npj Flexible Electronics2022，6，1： | 0 |
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