Prediction Intervals in Nonlinear Regression

By treating the nonlinear model as if it were linear in the parameterization θ in the neighbourhood of the least squares estimate θ, we construct two-sided nominally-q-prediction intervals by applying the usual linear model theory. The derivation of the truncated series expansion of the expected coverage of the prediction intervals at a feasible value of the parameter vector is described. The quadratic approximation of the expected coverage is then obtained for a two-parameter nonlinear model. Finally we show how we may construct the prediction intervals when a certain type of nonlinear transformation of the parameter vector has been applied.     

Adjustment of Prediction Intervals in Nonlinear Regression

By treating the nonlinear model as if it were linear in the parameterization θ in the neighbourhood of the least squares estimate θC, two-sided nominally-q-prediction intervals can be constructed by applying the usual linear model theory. The quadratic approximation of the expected coverage of the prediction intervals is derived for a p-parameter nonlinear model. An adjustment of the nominally-q-prediction intervals is proposed. It is shown that, to the extent that quadratic approximation is adequate, the actual expected coverage of the adjusted prediction intervals is q.     

Intervals for the assessment of measurement agreement: Similarities,differences, and consequences of incorrect interpretations

Several intervals have been proposed to quantify the agreement of two methods intended to measure the same quantity in the situation where only one measurement per method and subject is available. The limits of agreement are probably the most well‐known among these intervals, which are all based on the differences between the two measurement methods. The different meanings of the intervals are not always properly recognized in applications. However, at least for small‐to‐moderate sample sizes, the differences will be substantial. This is illustrated both using the width of the intervals and on probabilistic scales related to the definitions of the intervals. In particular, for small‐to‐moderate sample sizes, it is shown that limits of agreement and prediction intervals should not be used to make statements about the distribution of the differences between the two measurement methods or about a plausible range for all future differences. Care should therefore be taken to ensure the correct choice of the interval for the intended interpretation.     

利用神经网络对蛋白质家族进行预测

提出了一种利用神经网络为蛋白质家族建立模型的方法,这一方法的理论出发点是利用神经网络从一组同家族蛋白质序列中识别出共同的特征模式,建好的模型可用于预测蛋白质家族,使用这一方法。所能识别的模式在长度、位点等方面都不受限制。而且建模及预测过程中输入神经网络的蛋白质序列不需要作预对齐。对Pfam蛋白质库中的二十个家族运用此方法,预测的平均正确率达到了95．5％。     

植物Cation/H~+反向转运蛋白研究进展

CAX是一种通过质子梯度产生的能量运输协调再分配钙离子(Ca2+)等阳离子的转运蛋白,是Ca2+/Cation antiporter(CaCA)大家族的一个分化枝。植物CAXs属于CAX三大类的Ⅰ型CAX。大部分植物CAXs有11个跨膜区(TM)和5个典型的功能域,即N-端自抑制区域(NRR)、C-端功能区域、Ca2+功能域(CaD)、C功能域和D功能域。其中NRR存在于大部分CAX中,调节CAX的功能。以下综述了近年来国内外对CAX类蛋白的研究成果与进展,涉及到CAX家族的命名,亚家族的分类,CAX组织表达及亚细胞定位,特别是CAX的转运活性等研究。加强对CAX的研究对调节植物生长、提高农作物养分吸收和减轻土壤中污染物等有重要作用。     

Estimation and Tests of Mendelian Inheritance in Small Samples of Human Families

Estimation of parameters in human genetics is usually performed by Maximum Likelihood methods for large samples relying on asymptotic results. With the aim of evaluating the importance of the bias resulting from sample size, two sets of human family data have been analysed. The bias is not very important, but programs have been elaborated, giving better estimations. The tests of hypotheses from these estimations have also been considered.     

Intraindividual Scale Comparison in Clinical Diagnostic Methods: A Review of Elementary Methods

This text tries to summarize proposals on the statistical comparison of clinical measurement methods based on bivariate normally distributed outcome. It mainly concentrates on design adequate intraindividual comparison of variances in repeated measurements and reviews univariate graphical and numerical representations of corresponding deviations. The latter will be illustrated by the comparison of two cardiac imaging procedures in 28 probands.     

自花授粉作物杂交育种组合潜势的预测和比较

在黄花烟草Nicotiana russica中,开花期这一性状用V_5作亲本可能产生较大变异,无论是选择早开花的还是选择迟开花的,都有较大机会得到理想目标株系;对于株高这一性状,含有V(?)的组合可望有较大机会产生高于标准品种的株系。通过组合间育种潜势的比较,能了解各亲本中基因分布的基本情况,进而进行客观评价并对杂交组合做出取舍。试验证明,用一个组合的早期世代的参数m和D来预测高世代或纯系的育种潜势是可行的。     

赛黑桦不同半同胞家系种子活力比较

种子活力能够预测幼苗的生长势和适应性,可作为评价采种母树的重要指标。赛黑桦作为东北林区木质坚硬的树种之一,关于其种子活力研究尚未见报道。比较不同家系赛黑桦种子活力,对赛黑桦采种母树进行初步评价,可为赛黑桦优良家系的选择提供参考。本研究以赛黑桦蛟河、集安和珲春3个采种地共30个半同胞家系为试材,对采种地及家系间种子千粒重、发芽率、发芽势、发芽指数、活力指数、出苗率和幼苗健壮率等7个性状进行了方差分析、遗传力估算、多重比较、相关性分析,并利用主成分分析法对参试家系进行了综合评价。结果表明,赛黑桦种子活力指数和幼苗健壮率在不同采种地间的差异达到了显著或极显著水平;7个性状在不同家系间的差异均达到显著或极显著水平;除出苗率和幼苗健壮率外,各性状的家系遗传力均高于0.68;7个性状间均呈现显著或极显著的正相关;采用主成分分析法选择JH6、JA1、JA7、JH10、JH3、HC1和HC10等7个家系为优良家系,这些家系的种子千粒重、发芽率、发芽势、发芽指数、活力指数、出苗率和幼苗健壮率的平均值分别比总平均值高3.87%、30.29%、30.22%、31.99%、58.22%、11.88%和30.60%。初步认为这些优良家系的母树是赛黑桦采种的首选母树。     

Use of summary measures to adjust for informative missingness in repeated measures data with random effects

We discuss how to apply the conditional informative missing model of Wu and Bailey (1989, Biometrics 45, 939-955) to the setting where the probability of missing a visit depends on the random effects of the primary response in a time-dependent fashion. This includes the case where the probability of missing a visit depends on the true value of the primary response. Summary measures for missingness that are weighted sums of the indicators of missed visits are derived for these situations. These summary measures are then incorporated as covariates in a random effects model for the primary response. This approach is illustrated by analyzing data collected from a trial of heroin addicts where missed visits are informative about drug test results. Simulations of realistic experiments indicate that these time-dependent summary measures also work well under a variety of informative censoring models. These summary measures can achieve large reductions in estimation bias and mean squared errors relative to those obtained by using other summary measures.     

不同树龄水曲柳半同胞家系生长性状变异研究

为筛选优质的水曲柳种质资源,以吉林省三岔子林业局国家水曲柳良种基地的16年生水曲柳子代测定林75个半同胞家系为材料,分别在第4、11和16年对其树高、地径（胸径）和材积进行测定。方差分析结果表明,不同变异来源各指标均达极显著差异水平（P<0.01）;各指标表型变异系数变化范围为22.20%~63.30%,家系遗传力变化范围为0.796~0.981;相关性分析结果表明各指标间均呈极显著正相关;以材积为评价指标,按10%入选率对家系进行评价选择,初步筛选8个优良家系,入选的家系材积平均值比总平均值高0.007 m³,遗传增益为36.03%;该研究选出的优良家系可为良种登记提供基础,也可为种子园的改建提供材料。     

原发性肝癌患者术后癌因性疲乏的影响因素及其预测模型构建

摘要 目的：分析原发性肝癌患者术后癌因性疲乏（CRF）的影响因素并构建预测模型。方法：选取2020年1月～2023年1月湖南师范大学附属第一医院收治接受手术治疗的200例原发性肝癌患者,根据术后3个月是否存在CRF将患者分为CRF组（124例）和非CRF组（76例）。单因素和多因素Logistic回归分析影响原发性肝癌患者术后CRF的因素并构建其预测模型。通过受试者工作特征（ROC）曲线分析预测模型对原发性肝癌患者术后CRF的预测价值。结果：单因素分析显示,CRF组病程长于非CRF组,Child-Pugh分级B级、美国东部肿瘤协作组功能状态（ECOG）评分1～2分、辅助化疗、医疗付费方式自费、抑郁/焦虑比例高于非CRF组,文化程度高中及以上、家庭月收入＞3000元、高度社会支持度比例低于非CRF组（P＜0.05）。多因素Logistic回归分析显示,病程延长、Child-Pugh分级B级、ECOG评分1～2分、辅助化疗、医疗付费方式自费、抑郁/焦虑为影响原发性肝癌患者术后CRF的独立危险因素,家庭月收入＞3000元、高度社会支持为独立保护因素（P＜0.05）。原发性肝癌患者术后CRF的预测模型方程：Logit（P）=P/1-P=-1.252+0.409×病程+0.839×Child-Pugh分级+1.378×ECOG评分+1.055×辅助化疗+1.476×医疗付费方式-0.793×家庭月收入+0.883×抑郁/焦虑-1.260×社会支持度。霍斯默-莱梅肖检验P＞0.05。ROC曲线分析显示,模型预测原发性肝癌患者术后CRF的曲线下面积为0.910,敏感度为87.10%,特异度为85.53%。结论：病程、Child-Pugh分级、ECOG评分、辅助化疗、医疗付费方式、抑郁/焦虑、家庭月收入、社会支持度为影响原发性肝癌患者术后CRF的因素,基于此构建的预测模型对原发性肝癌患者术后CRF的预测价值较高,可能有助于临床早期发现和干预原发性肝癌患者术后CRF,以改善患者预后。     

Prediction of the deleterious nsSNPs in ABCB transporters

The non-synonymous SNPs (nsSNPs) in coding regions, neutral or deleterious, could lead to the alteration of the function or structure of proteins. We have developed the computational models to analyze the deleterious nsSNPs in the transporters and predict ones in ABCB (ATP-binding cassette B) transporters of interest. The RPLS (ridge partial least square) and LDA (linear discriminant analysis) methods were applied to the problem, by training on a selection of datasets from a specified source, i.e., human transporters. The best combination of datasets and prediction attributes was ascertained. The prediction accuracy of the theoretical RPLS model for the training and testing sets is 84.8% and 80.4%, respectively (LDA: 84.3% and 80.4%), which indicates the models are reasonable and may be helpful for pharmacogenetics studies.     

植物microRNA的生物信息学预测与分析

microRNAs(miRNAs)是一类广泛存在于真核生物中调控基因转录后表达的非编码小分子RNA。大量研究表明,miRNA在调节多种生物途径中起着重要的作用,采用生物信息学方法预测与分析miRNA是当前发现和鉴定植物miRNA的重要策略之一。研究内容总结了生物信息学预测植物miRNA及其靶基因的方法策略,阐述了生物信息学在植物miRNA研究中的重要作用,为今后的研究奠定了基础。     

Fast approximations of pseudo-observations in the context of right censoring and interval censoring

In the context of right-censored and interval-censored data, we develop asymptotic formulas to compute pseudo-observations for the survival function and the restricted mean survival time (RMST). These formulas are based on the original estimators and do not involve computation of the jackknife estimators. For right-censored data, Von Mises expansions of the Kaplan–Meier estimator are used to derive the pseudo-observations. For interval-censored data, a general class of parametric models for the survival function is studied. An asymptotic representation of the pseudo-observations is derived involving the Hessian matrix and the score vector. Theoretical results that justify the use of pseudo-observations in regression are also derived. The formula is illustrated on the piecewise-constant-hazard model for the RMST. The proposed approximations are extremely accurate, even for small sample sizes, as illustrated by Monte Carlo simulations and real data. We also study the gain in terms of computation time, as compared to the original jackknife method, which can be substantial for a large dataset.     

白内障超声乳化联合人工晶状体植入术后感染性眼内炎的影响因素及其预测模型构建

摘要 目的：探讨白内障超声乳化联合人工晶状体植入术后感染性眼内炎的影响因素及其预测模型构建。方法：回顾性分析2015年2月至2023年2月我院收治的12308例白内障患者的临床资料,所有患者均行白内障超声乳化联合人工晶状体植入手术治疗,统计术后感染性眼内炎发生情况。采用多因素Logistic回归模型分析白内障超声乳化联合人工晶状体植入术后感染性眼内炎的影响因素,根据回归模型构建预测模型,采用受试者工作特征（ROC）曲线验证预测模型的预测效能。结果：12308例患者中发生感染性眼内炎32例（0.26%）。单因素分析结果显示感染组年龄≥70岁、合并糖尿病、手术时间≥30 min、手术切口≥3.2 mm、植入PMMA人工晶体、后囊膜破裂比例高于对照组（P＜0.05）,术中预防性使用抗生素、晶状体后冲洗比例低于对照组（P＜0.05）。多因素Logistic回归模型分析显示年龄≥70岁、合并糖尿病、后囊膜破裂、植入PMMA人工晶体是白内障超声乳化联合人工晶体植入术后感染性眼内炎的危险因素（P＜0.05）,术中预防性使用抗生素、晶状体后冲洗是保护因素（P＜0.05）。以Logistic回归模型结果保留变量构建预测模型,Hosmer-Lemeshow拟合优度检验P＞0.05。ROC分析该模型预测白内障超声乳化联合人工晶体植入术后感染性眼内炎的曲线下面积为0.832,灵敏度、特异度分别为81.25%、85.12%。结论：年龄≥70岁、合并糖尿病、后囊膜破裂、植入PMMA人工晶状体是术后感染性眼内炎的危险因素,术中预防性使用抗生素、晶状体后冲洗可降低感染性眼内炎发病风险。根据多因素Logistic回归分析构建的预测模型对感染性眼内炎的预测能效较好。     

Genetic Variability of Adult Body Mass Index: A Longitudinal Assessment in Framingham Families

Objective: To explore the contribution of genetics to the mean, SD, maximum value, maximum less the mean, and change over time in body mass index (BMI) and the residual of body weight after adjustment for height. BMI is frequently used as a general indicator of obesity because of its ease and reliability in ascertainment. Cross‐sectional twin and family studies have shown a moderate‐to‐substantial genetic component for BMI. However, the contribution of genetics to the long‐term average, variability, or change over time in BMI is less clear. Research Methods and Procedures: Longitudinal data from the Framingham heart study were used to create pedigrees of age‐matched individuals. Heritability estimates were derived using variance‐decomposition methods on a total of 1051 individuals from 380 extended pedigrees followed for a period of 20 years. All subjects were followed from approximately age 35 to 55 years. Results: Moderate heritability estimates were found for the mean BMI (h² = 0.37), maximum BMI (h² = 0.40), and the mean residual of body weight (h² = 0.36). Low heritability estimates (h² ? 0.20) were found for the maximum less the mean in BMI and the SDs of BMI and residual of body weight. No additive genetic contribution was found for the average change over time in BMI or the residual of body weight. Discussion: These findings suggest that there is a significant genetic component for the magnitude of BMI throughout an individual's middle‐adult years; however, little evidence was found for a genetic contribution to the variability or rate of change in an individual's BMI.     

Precision Intervals for Estimates of the Difference in Success Rates for Binary Random Variables Based on the Permutation Principle

Fisher's exact test is a very commonly applied test in clinical trials with a binary outcome variable (e.g. success/failure). However confidence statements about the difference of success rates are usually based on the normal approximation. This may sometimes lead to the confusing statement that the test is statistically significant at a prespecified level while the corresponding confidence interval includes the zero difference and vice versa. Here, we construct precision intervals for the difference of success rates from two independent samples based on the permutation principle which are in perfect agreement with the discrete (permutation) test and compare it to examples from the literature. APL programs are provided.     

基于转录终点序列特征预测大肠杆菌sRNA

细菌sRNA是一类长度在40～500nt的调控RNA,在细菌与环境相互作用中发挥重要功能,因此,细菌sRNA识别研究具有重要意义。然而,与蛋白编码基因具有易于识别的特征不同,目前细菌sRNA识别仍是一件比较困难的事。此方法介绍了一个基于已知细菌sRNA转录终点的碱基频率矩阵来识别sRNA的预测策略,并在大肠杆菌K-12 MG1655中进行了sRNA的预测。结果表明,该模型在独立测试集中具有较高的特异性和阳性检出率,因此,这一方法将为实验发现细菌sRNA提供较好的生物信息学支持。