Tests of significance for point-biserial rank correlation coefficients in the presence of ties

This paper deals with exact and asymptotic tests of significance of the point-biserial rank correlations of the KENDALL and SPEARMAN tests when ties are present and mid-ranks are assigned to tied values.     

Jumping ability is related to change of direction ability in elite handball players

PurposeThis study investigated the relationship between vertical and horizontal jumping ability and change of direction (COD) to measure athletic performance in 51 elite male handball players.Scope.Countermovement jump (CMJ), peak power, and standing long jump (SLJ) were measured. Participants performed a 20-m sprint test (time measured at 5, 10, and 20 m) and a zigzag test (COD: 135°, 90°, and 45°). The COD deficit, an index of the time required for COD, was calculated. The correlations between CMJ height and zigzag test times were relatively large (at 135°, r =  − 0.607; at 90°, r =  − 0.594; at 45°, r =  − 0.613; p < 0.01), whereas those between CMJ height and COD deficit were moderate (at 135°, r =  − 0.399, p < 0.01; at 90°, r =  − 0.350, p < 0.05; at 45°, r =  − 0.323, p < 0.05). SLJ showed a negative moderate correlation with COD deficit (at 135°, r =  − 0.439, p < 0.01; at 90°, r =  − 0.469, p < 0.01; at 45°, r =  − 0.380, p < 0.01).ConclusionsThis study is the first to analyse SLJ ability and COD deficit parameters of handball players. We found that SLJ ability is moderately related to COD time and deficit; therefore, SLJ measurement may be a useful predictor of athletic performance.     

A robust correlation estimator and nonlinear recurrent model to infer genetic interactions in Saccharomyces cerevisiae and pathways of pulmonary disease in Homo sapiens

In order to identify genes involved in complex diseases, it is crucial to study the genetic interactions at the systems biology level. By utilizing modern high throughput microarray technology, it has become feasible to obtain gene expressions data and turn it into knowledge that explains the regulatory behavior of genes. In this study, an unsupervised nonlinear model was proposed to infer gene regulatory networks on a genome-wide scale. The proposed model consists of two components, a robust correlation estimator and a nonlinear recurrent model. The robust correlation estimator was used to initialize the parameters of the nonlinear recurrent curve-fitting model. Then the initialized model was used to fit the microarray data. The model was used to simulate the underlying nonlinear regulatory mechanisms in biological organisms. The proposed algorithm was applied to infer the regulatory mechanisms of the general network in Saccharomyces cerevisiae and the pulmonary disease pathways in Homo sapiens. The proposed algorithm requires no prior biological knowledge to predict linkages between genes. The prediction results were checked against true positive links obtained from the YEASTRACT database, the TRANSFAC database, and the KEGG database. By checking the results with known interactions, we showed that the proposed algorithm could determine some meaningful pathways, many of which are supported by the existing literature.     

旅游干扰对历山亚高山草甸优势种群种间相关性的影响

基于2×2列联表,应用方差比率法、χ2检验、Pearson相关系数检验及Spearm an秩相关系数检验等数量分析方法研究了旅游干扰对山西历山舜王坪亚高山草甸种间关联程度的影响。结果表明:(1)不同旅游距离带的联结指数(VR)均大于1,但统计量W均界于χ2分布的上下临界值之间。群落总体呈正关联,但联结性较弱,种的分布相对独立。(2)随着距游径距离的增加,4条不同旅游距离带的联结指数(VR)呈下降趋势;正负关联比有所增加,2χ检验显著率、Pearson相关检验显著率和Spearm an秩相关检验显著率都明显下降,说明旅游干扰对舜王坪亚高山草甸种间关联程度产生了一定的影响,距离游径越远,种间关联越趋于随机性,但这种影响尚未引起种间联结性的改变。(3)χ2检验与Pearson相关系数检验、Spearm an秩相关系数检验结果用来刻划种间相关性具有一定的相似之处,但仍存在一定差异,结合使用效果更好。与Pearson相关检验相比,Spearm an秩相关检验更具灵敏性。4)本研究结果支持随着群落演替进程的发展,群落种群总体向着无关联发展的观点。     

Analysis on regulatory network linked to Hpa gene in invasion and metastasis of colon cancer

Our purpose was to discuss the biological function of Hpa gene and its regulatory network in invasion and metastasis of colon cancer. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes database were used to perform functional annotation and pathway analysis on Hpa gene. Gene Ontology analysis results showed that Hpa plays a significant role in cellular component, molecular function and biological process; and combined with Kyoto Encyclopedia of Genes and Genomes database, regulatory network of angiogenesis of colon cancer was drawn out. Through analysis of regulatory network linked to angiogenesis in invasion and metastasis of colon cancer, the study lays foundation for further prevention, diagnosis and treatment of colon cancer.     

Selection of sires to reduce sampling variance in the estimates of heritability by half-sib correlation

Summary Standard methods to estimate heritability by half-sib correlation are biased if selection has operated in the parental generation. In this paper a simple method to correct for selection of animals used as sires is described. By selection of both the top and the bottom ranking sires, the sampling variances of the corrected estimates of heritability are substantially reduced. Algebraic expressions to predict the sampling variance of the estimates of heritability using selected sires are derived. Theoretical predictions were checked by Monte-Carlo simulation. The results may have application in the design of experiments to estimate heritabilities.     

Partition coefficients of the iron(III) complexes of pyridoxal isonicotinoyl hydrazone and its analogs and the correlation to iron chelation efficacy

Pyridoxal isonicotinoyl hydrazone and its analogs are orally effective Fe(III) chelators which show potential as drugs to treat iron overload disease. The present investigation describes the measurement of the partition coefficient of the apochelator and Fe(III) complex of 20 of these ligands. These measurements have been done to investigate the relationship between lipophilicity and the efficacy of iron chelation in rabbit reticulocytes loaded with non-heme ⁵⁹Fe. The results demonstrate a linear relationship between the partition coefficient (P) of the apochelator and its Fe(III) complex, and a simple equation has been derived relating these two parameters. Experimental data in the literature are in agreement with the equation. The relationship of the partition coefficients of the iron chelators and of their Fe(III) complexes to the effectiveness of the ligands in mobilizing iron in vitro and in vivo is also discussed.     

Using conditional power of network meta‐analysis (NMA) to inform the design of future clinical trials

Clinical trials are typically designed with an aim to reach sufficient power to test a hypothesis about relative effectiveness of two or more interventions. Their role in informing evidence‐based decision‐making demands, however, that they are considered in the context of the existing evidence. Consequently, their planning can be informed by characteristics of relevant systematic reviews and meta‐analyses. In the presence of multiple competing interventions the evidence base has the form of a network of trials, which provides information not only about the required sample size but also about the interventions that should be compared in a future trial. In this paper we present a methodology to evaluate the impact of new studies, their information size, the comparisons involved, and the anticipated heterogeneity on the conditional power (CP) of the updated network meta‐analysis. The methods presented are an extension of the idea of CP initially suggested for a pairwise meta‐analysis and we show how to estimate the required sample size using various combinations of direct and indirect evidence in future trials. We apply the methods to two previously published networks and we show that CP for a treatment comparison is dependent on the magnitude of heterogeneity and the ratio of direct to indirect information in existing and future trials for that comparison. Our methodology can help investigators calculate the required sample size under different assumptions about heterogeneity and make decisions about the number and design of future studies (set of treatments compared).     

Using Knowledge of Protein Structural Constraints to Predict the Evolution of HIV-1

The high levels of sequence diversity and rapid rates of evolution of HIV-1 represent the main challenges for developing effective therapies. However, there are constraints imposed by the three-dimensional protein structure that affect the sequence space accessible to the evolution of HIV-1. Here, we present a strategy for predicting the set of possible amino acid replacements in HIV. Our approach is based on the identification of likely amino acid changes in the context of these structural constraints using environment-specific substitution matrices as well as considering the physical constraints imposed by local structure. Assessment of the power of various published algorithms in predicting the evolution of HIV-1 Gag P17 shows that it is possible to use these methods to make accurate predictions of the sequence diversity. Our own method, SubFit, uses knowledge of local structural constraints; it achieves similar prediction success with the best-performing methods. We also show that erroneous predictions are largely due to infrequently occurring amino acids that will probably have severe fitness costs for the protein. Future improvements; for example, incorporating covariation and immunological constraints will permit more reliable prediction of viral evolution.