Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice

Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.In this study,113 indica rice varieties(V)and their 565 testcross hybrids(TC)were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.The original traits and general combining ability of the parents,as well as the original traits and midparent heterosis of TC,were subjected to genome-wide association analysis.In total,381 primary significantly associated loci(SAL)and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.Among these loci,322 candidate genes located within or nearby the SALs were screened,204 of which were cloned genes.A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.All the SALs were used to construct genetic networks,in which 91 pleiotropic loci were investigated.Additionally,we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs,primary SALs,secondary SALs or epistatic effect SALs as covariates.Although the prediction accuracies of the four models were generally not significantly different in the TC dataset,the incorporation of primary SALs,secondary SALs,and epistatic effect SALs significantly improved the prediction accuracies of 5(26%),3(16%),and 11(58%)traits in the V dataset,respectively.These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.

Casual associations between blood metabolites and colon cancer

BACKGROUND Limited knowledge exists regarding the casual associations linking blood metabolites and the risk of developing colorectal cancer.AIM To investigate causal associations between blood metabolites and colon cancer.METHODS The study utilized a two-sample Mendelian randomization(MR)analysis to investigate the causal impact of 486 blood metabolites on colorectal cancer.The primary method of analysis used was the inverse variance weighted model.To further validate the results several sensitivity analyses were performed,including Cochran's Q test,MR-Egger intercept test,and MR robust adjusted profile score.These additional analyses were conducted to ensure the reliability and robustness of the findings.RESULTS After rigorous selection for genetic variation,486 blood metabolites were included in the MR analysis.We found Mannose[odds ratio(OR)=2.09(1.10-3.97),P=0.024],N-acetylglycine[OR=3.14(1.78-5.53),P=7.54×10^(-8)],X-11593-O-methylascorbate[OR=1.68(1.04-2.72),P=0.034],1-arachidonoylglycerophosphocholine[OR=4.23(2.51-7.12),P=6.35×10^(-8)]and 1-arachidonoylglycerophosphoethanolamine 4[OR=3.99(1.17-13.54),P=0.027]were positively causally associated with colorectal cancer,and we also found a negative causal relationship between Tyrosine[OR=0.08(0.01-0.63),P=0.014],Urate[OR=0.25(0.10-0.62),P=0.003],N-acetylglycine[0.73(0.54-0.98),P=0.033],X-12092[OR=0.89(0.81-0.99),P=0.028],Succinylcarnitine[OR=0.48(0.27-0.84),P=0.09]with colorectal cancer.A series of sensitivity analyses were performed to confirm the rigidity of the results.CONCLUSION This study showed a causal relationship between 10 blood metabolites and colorectal cancer,of which 5 blood metabolites were found to be causal for the development of colorectal cancer and were confirmed as risk factors.The other five blood metabolites are protective factors.

Genetic Parameters and Genome-Wide Association Studies for Body Size Traits of Shuxuan Cattle in China

In domestic cattle,the body size traits have important implications in terms of breed characteristics and production performance.Shuxuan cattle is a dual-purpose breed mainly raised in Sichuan province,China,for which we have known less about the genetic parameters and underlying candidate genes in relation to the body size traits.In this study,we obtained the genome-wide single nucleotide polymorphisms(SNPs)using the Illumina Bovine BeadChip in 275 Shuxuan cattle.These SNPs were first used for estimating genetic parameters for the withers height(WH)and diagonal body length(BL).Using the bivariate animal model,the estimates(±standard error)of heritabilities were 0.71±0.22 and 0.49±0.29 for BL,and their genetic correlation was 0.64±0.37.Second,the genome-wide association study(GWAS)was performed.However,these did not result into genome-wide significant SNPs for both WH and BL traits.According to a less stringent suggestive significance,some positional candidate genes were found,and some of them(such as FAM110B,TAS1R2,PAX3,and FHIT)were previously reported in literature to be associated with body size traits in cattle.In conclusion,we estimated the genetic parameters in Shuxuan cattle using genomic information for the first time,which are required for implementing the genomic selection programs in the future.

Exploration of the Impact of Language Proficiency on Vocabulary Association Patterns in English Language Education

This paper explores the lexical association patterns of English as a second language and their relationship with language proficiency.Through the vocabulary association test,the study analyzes the differences in vocabulary association between learners with different language levels.The participants were 100 non-native English-speaking un-dergraduate students from a top 200 university,such as the University of Nottingham,and a university outside the top 200,such as the University of Aberdeen;the two groups of learners differed in their vocabulary size and learning style.It was found that the two groups of learners differed significantly in vocabulary size,language background,and learning experience.In addition,the study raises three core questions:first,learners’lexical association patterns,second,dif-ferences in association among learners with different language proficiency levels,and third,other variables that affect vocabulary association ability.The limitations of the study are that reaction time was not measured and the influence of native language background on word association was not fully considered;future research should further explore these aspects.

Application Comparison of Association Rules and C4.5 Rules in Land Evaluation

Association rules and C4.5 rules can overcome the shortage of the traditional land evaluation methods and improve the intelligibility and efficiency of the land evaluation knowledge.In order to compare these two kinds of classification rules in the application,two fuzzy classifiers were established by combining with fuzzy decision algorithm especially based on Second General Soil Survey of Guangdong Province.The results of experiments demonstrated that the fuzzy classifier based on association rules obtain a higher accuracy rate,but with more complex calculation process and more computational overhead;the fuzzy classifier based on C4.5 rules obtain a slightly lower accuracy,but with fast computation and simpler calculation.

基于OPC UA的分布式数据采集处理系统架构研究

随着物联网与互联网融合的不断深化,感知层与应用层之间的互联互通要求不断提高。针对现有数据采集系统存在的规范性、扩展性和适应性不足的问题,文章提出一套基于对象连接与嵌入过程控制统一架构(object linking and embedding for process control unified architecture,OPC UA)协议的分布式数据采集处理系统架构。对数据采集处理系统各个模块进行功能解耦和架构重组,分别介绍该系统硬件和软件架构;针对发布订阅模式下负载的特异性,提出一种改进的适用于OPC UA分布式订阅的负载均衡算法;最后在某车企实例验证该系统架构。结果表明,基于OPC UA的分布式数据采集处理系统数据采集处理效果良好,证明了该系统架构的可行性及有效性。

基于OPC UA的虚实结合实验设计与实践

OPCUA是一种面向未来的工业通信技术,是实现智能制造的关键技术之一,在工业网络系统中得到越来越广泛的应用。为促进教学资源同步技术发展,以OPCUA技术为出发点,设计了基于OPCUA通信的客户端仿真、系统虚拟仿真、实践操作三个进阶实验项目。项目开发充分利用行业已有客户端测试软件和虚拟仿真软件资源,兼顾线上、线下学习,内容由基础到综合、虚实结合,旨在提升学生新技术应用能力和自主创新能力,更好地服务于智能制造转型升级和发展,为相关专业的实践教学及资源开发提供参考。

基于OPC UA的纤维缠绕机信息模型开发和应用

为实现对复合材料纤维缠绕机生产过程的监测,以缠绕机及其辅助设备为研究对象,针对实际加工设备的多样性造成的加工数据采集的异构性,基于OPC UA建立缠绕机的信息模型架构。根据OPC基金会发布的OPC UA规范和相关的行业标准,建立纤维缠绕机系统的信息模型和实例化。基于开源项目open62541,导入编译后的缠绕机的信息模型代码,自定义开发出符合使用规范的OPC UA服务器,然后利用UA客户端实现对服务器的连接,客户端能够通过服务器查询系统的加工数据,解决加工数据的异构性问题以达到监测缠绕机生产加工过程的目的;最后验证了建立的纤维缠绕机信息模型能够正确导入到开源项目open62541中,实现了加工数据监测。

不同肠内营养制剂用于2型糖尿病患者对血糖及血清UA、PA、ALB的影响

目的探究康全力、能全力与瑞能三种不同肠内营养制剂用于2型糖尿病(T2DM)患者对血糖及血清尿酸(UA)、前白蛋白(PA)、白蛋白(ALB)等的影响。方法选取2020年1月至2023年3月于涟水县人民医院重症医学科内分泌与代谢性疾病科治疗的99例T2DM患者为研究对象,按非随机临床同期对照研究及患者自愿原则分为康全力组、能全力组和瑞能组,每组各33例。三组患者分别给予康全力、能全力和瑞能三种不同肠内营养制剂治疗,均连续治疗2个月,比较糖代谢、营养指标、血脂、炎症因子水平和不良反应发生情况。结果治疗后三组糖代谢指标均显著降低,其中康全力组患者治疗后糖化血红蛋白(HbA1c)、空腹血糖(FPG)、餐后2 h血糖(2hPG)、空腹胰岛素(FINS)、胰岛素抵抗指数(HOMA-IR)与能全力组和瑞能组相比均显著降低(P<0.05);治疗后三组血清UA明显下降,PA和ALB水平明显升高(P<0.05),但组间差异无统计学意义(P>0.05);治疗后三组HDL-C均显著升高,康全力组LDL-C、TC和TG均显著降低(P<0.05),能全力组、瑞能组LDL-C、TC和TG未见显著改变(P>0.05),其中康全力组治疗后HDL-C与另外两组相比显著高,LDL-C与另外两组相比显著低,TC和TG与瑞能组相比显著低(P<0.05);治疗后三组IL-6、CRP水平与治疗前相比均显著降低(P<0.05),治疗后康全力组、能全力组IL-6和CRP水平与瑞能组相比显著低(P<0.05);治疗后康全力组、能全力组和瑞能组的不良反应发生总概率为12.12%、21.21%和15.15%,差异无统计学意义(P>0.05)。结论康全力在调节糖脂代谢、缓解炎症反应方面效果较其他肠内营养制剂更突出。

Association of HLA-B Alleles With Human Immunodeficiency Virus Type 1 Infection in the Yi Ethnic Group in Sichuan Province

Objective To determine the distribution of HLA-B alleles in the Chinese Yi ethnic group and its association with HIV infection. Methods One hundred and six unrelated healthy HIV negative and 73 HIV positive Chinese Yi ethnic individuals were typed by PCR-SSP. Results The frequency of alleles B*07, B*35, and B*46 were increased in HTV-1 -positive subjects, whereas the alleles B*55, B*44 and B*78 were absent in the HIV-infected persons studied. The B*46 allele was present in a significantly higher gene frequency among HIV-1-positive individuals (P=0.02, OR=3.32, 95% CI=1.13-9.78) compared with control subjects. Conclusion HLA-B*46 may be associated with its susceptibility to HIV-1 infections.

A multivariate partial least squares approach to joint association analysis for multiple correlated traits

Many complex traits are highly correlated rather than independent. By taking the correlation structure of multiple traits into account, joint association analyses can achieve both higher statistical power and more accurate estimation. To develop a statistical approach to joint association analysis that includes allele detection and genetic effect estimation, we combined multivariate partial least squares regression with variable selection strategies and selected the optimal model using the Bayesian Information Criterion(BIC). We then performed extensive simulations under varying heritabilities and sample sizes to compare the performance achieved using our method with those obtained by single-trait multilocus methods. Joint association analysis has measurable advantages over single-trait methods, as it exhibits superior gene detection power, especially for pleiotropic genes. Sample size, heritability,polymorphic information content(PIC), and magnitude of gene effects influence the statistical power, accuracy and precision of effect estimation by the joint association analysis.

Determination of Residual Feed Intake and Its Associations with Single Nucleotide Polymorphism in Chickens

Marker assisted selection （MAS） for residual feed intake （RFI） is considered to be one of the powerful means to improve feed conversion efficiency, and therefore reduce production costs. To test the inner relationship among body compositions, growth traits and RFI, four models were proposed to assess the extensively explanatory variables accounting for partial variables in feed intake besides metabolic body weight and growth rate. As a result, the original model （Koch＇s model） had the lowest R2 （80.78%） and the highest Bayesian information criterion （1 323.3） value among the four models. Moreover, the effects on RFI caused by single nucleotide polymorphisms （SNPs） were assessed in this study. Twelve SNPs from 7 candidate genes were genotyped in 2 Chinese native strains, rs14743490 of RPLP2 gene showed suggestively significant association with initial body weight in both strains （P〈0.10）. rs15047274 of TAF15 was significantly associated with growth weight, final weight, and feed intake （P〈0.05） in N301 strain, in contrast, it was only suggestively significant associated with feed intake （P〈0.10） in N414 strain, rs15869967 was significantly associated with RFI in N414 strain but not in N301 strain. This study has identified potential genetic markers suitable for MAS in improving the above mentioned traits, but these associations need to be rectified in other larger populations in future.

Empirical Euclidean likelihood for general estimating equations under association dependence

Empirical Euclidean likelihood for general estimating equations for association dependent processes is investigated. The strong consistency and asymptotic normality of the blockwise maximum empirical Euclidean likelihood estimator are presented. We show that it is more efficient than estimator without blocking. The blockwise empirical Euclidean log-likelihood ratio asymptotically follows a chi-square distribution.

Post electrical or lightning injury syndrome: a proposal for an American Psychiatric Association's Diagnostic and Statistical Manual formulation with implications for treatment

In the past, victims of electrical and lightning injuries have been assessed in a manner lacking a system- atic formulation, and against ad hoc criteria, particularly in the area of neuropsychological disability. In this manner patients have, for example, only been partially treated, been poorly or incorrectly diagnosed, and have been denied the full benefit of compensation for their injuries. This paper contains a proposal for diagnostic criteria particularly for the neuropsychological aspects of the post injury syndrome. It pays attention to widely published consistent descriptions of the syndrome, and a new cluster analysis of post electrical injury patients. It formulates a proposal which could be incorporated into future editions of the American Psychiatric Association＇s Diagnostic and Statistical Manual （DSM）. The major neuropsycholog- ical consequences include neurocognitive dysfunction, and memory subgroup dysfunction, with ongoing consequences, and sometimes including progressive or delayed psychiatric, cognitive, and/or neurological symptoms. The proposed diagnostic criteria insist on a demonstrated context for the injury, both specifying the shock circumstance, and also physical consequences. It allows for a certain delay in onset of symptoms. It recognizes exclusory conditions. The outcome is a proposal for a DSM classification for the post electrical or lightning injury syndrome. This proposal is considered important for grounding patient treatment, and for further treatment trials. Options for treatment in electrical or lightning injury are summarised, and future trials are foreshadowed.

User Association in Heterogeneous Network with Dual Connectivity and Constrained Backhaul

A novel user association model for heterogeneous network(Het Net) with dual connectivity(DC) and constrained backhaul is proposed in this paper, where not only the best combination of serving macro cell and small cell for each user to associate is selected but also the optimal traffi c split between the macro cell and small cell is determined to enhance both radio resource effi ciency and backhaul capacity utilization. To solve this optimization problem, an intuitive algorithm based on iteratively solving two sub-problems is proposed. One sub-problem is a binary integer programming problem and a corresponding greedy algorithm is proposed, while the other sub-problem is a simple linear programming problem and can be easily solved. Numerical results show that the proposed model and algorithm can achieve better radio resource effi ciency and backhaul capacity utilization compared with user association in Het Net without DC, which validate the capacity enhancement potentials of radio resource coordination in Het Net with DC.

GEOMETRIC CONSTRUCTION OF ASSOCIATION SCHEMES FROM DEGENERATE QUADRICS INPROJECTIVE SPACES PG(2ν+δ+ι-1, Fq) FOR q ODD

Let Fq be a finite field with q elements, where q is a power of an odd prime,In this paperl the authors consider a projective space PG(2v + δ + l, Fq) with dimension 2v + δ + l, partitioned into an affine space AG(2v + δ + l, Fq) of dimension 2v + δ + l and a hyperplane H = PG(2v + δ + l - 1, Fq) of dimension 2v + δ + l - 1 at infinity, where l ≠0.The points of the hyperplane H are next partitioned into four subsets. A pair of points a and b of the affine space is defined to belong to class i if the line ab meets the subsct i of H. Finally, a family of four-class association schemes are constructed, and parameters are also computed.

Visualizing Association Rules Using Linked Matrix,Graph, and Detail Views

Although association rule mining is an important pattern recognition and data analysis technique, extracting and finding significant rules from a large collection has always been challenging. The ability of information visualization to enable users to gain an understanding of high dimensional and large-scale data can play a major role in the exploration, identification, and interpretation of association rules. In this paper, we propose a method that provides multiple views of the association rules, linked together through a filtering mechanism. A visual inspection of the entire association rule set is enabled within a matrix view. Items of interest can be selected, resulting in their corresponding association rules being shown in a graph view. At any time, individual rules can be selected in either view, resulting in their information being shown in the detail view. The fundamental premise in this work is that by providing such a visual and interactive representation of the association rules, users will be able to find important rules quickly and easily, even as the number of rules that must be inspected becomes large. A user evaluation was conducted which validates this premise.

Comparison of dimension reduction-based logistic regression models for case-control genome-wide association study:principal components analysis vs.partial least squares

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.

No evidence for a genetic association between female mating preference and male secondary sexual trait in a Lake Victoria cichlid fish

Sexual selection by female mating preference for male nuptial coloration has been suggested as a driving force in the rapid speciation of Lake Victoria cichlid fish. This process could have been facilitated or accelerated by genetic associations between female preference loci and male coloration loci. Preferences, as well as coloration, are heritable traits and are probably determined by more than one gene. However, little is known about potential genetic associations between these traits. In turbid water, we found a population that is variable in male nuptial coloration from blue to yellow to red. Males at the extreme ends of the phenotype distribution resemble a reproductively isolated species pair in clear water that has diverged into one species with blue-grey males and one species with bright red males. Females of the turbid water population vary in mating preference coinciding with the male phenotype distribution. For the current study, these females were mated to blue males. We measured the coloration of the sires and male offspring. Parents-offspring regression showed that the sires did not affect male offspring coloration, which confirms earlier findings that the blue species breeds true. In contrast, male offspring coloration was determined by the identity of the dams, which suggests that there is heritable variation in male color genes between females. However, we found that mating preferences of the dams were not correlated with male offspring coloration. Thus, there is no evidence for strong genetic linkage between mating preference and the preferred trait in this population [Current Zoology 56 （1）： 57-64 2010].

Validation of the Red Pericarp Gene from 419 Rice Landraces in Guangxi via Genome-wide Association Studies

Rice has different colors of pericarp, such as red, white and black. Red rice pericarp is rich in proanthocyanins, which have antioxidant properties and are beneficial to human health. In the present study, we analyzed the red-pericarp gene Rc of 419 rice landraces in Guangxi by genome-wide association study （GWAS）, and validated that the Rc gene regulated the red periearp trait in flee. By analyzing the genomie DNA of 97 red-pericarp flee eultivars, we identified two new alleles in C139 and C323. Then, the exons of Rcc＇9 and Rcc were sequenced with Sanger method, and the results demonstrated that the natural mutations within Re ene resulted in the two alleles Rcc and Rcc.