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Inference and Sample Size Calculations Based on Statistical Tests in aNegative Binomial Distribution for Differential Gene Expression in RNAseqData 基于RNAseqData中差异基因负二项分布统计检验的推断和样本量计算
Pub Date : 2017-01-30 DOI: 10.4172/2155-6180.1000332
Xiaohong Li, N. Cooper, Y. Shyr, Dongfeng Wu, E. Rouchka, R. Gill, T. O’Toole, G. Brock, S. Rai
The high throughput RNA sequencing (RNA-seq) technology has become the popular method of choice for transcriptomics and the detection of differentially expressed genes. Sample size calculations for RNA-seq experimental design are an important consideration in biological research and clinical trials. Currently, the sample size formulas derived from the Wald and the likelihood ratio statistical tests with a Poisson distribution to model RNA-seq data have been developed. However, since the mean read counts in the real RNA-seq data are not equal to the variance, an extended method to calculate sample sizes based on a negative binomial distribution using an exact test statistic was proposed by Li et al. in 2013. In this study, we alternatively derive five sample size calculation methods based on the negative binomial distribution using the Wald test, the log-transformed Wald test and the log-likelihood ratio test statistics. A comparison of our five methods and an existing method was performed by calculating the sample sizes and the simulated power in different scenarios. We first calculated the sample sizes for testing a single gene using the six methods given a nominal significance level α at 0.05 and 80% power. Then, we calculated the sample sizes for testing multiple genes given a false discovery rate (FDR) at 0.05 and 0.10. The empirical power and true prognostic genes for differential gene expression analysis corresponding to the estimated sample sizes from the six methods are also estimated via the simulation studies. Using the sample size formulas derived from log-transformed and Wald-based tests, we observed smaller sample properties while maintaining the nominal power close to or higher than 80% in all the settings compared to other methods. Moreover, the Wald test based sample size calculation method is easier to compute and faster in an RNA-seq experimental design.
高通量RNA测序(RNA-seq)技术已成为转录组学和差异表达基因检测的热门方法。RNA-seq实验设计的样本量计算是生物学研究和临床试验中的一个重要考虑因素。目前,已经开发了由Wald和泊松分布的似然比统计检验导出的样本量公式来模拟RNA-seq数据。然而,由于真实RNA-seq数据中的平均读取计数不等于方差,Li等人于2013年提出了一种基于负二项分布的扩展方法,使用精确检验统计量计算样本容量。在本研究中,我们分别使用Wald检验、对数变换Wald检验和对数似然比检验统计量推导了五种基于负二项分布的样本量计算方法。通过计算不同场景下的样本量和模拟功率,将五种方法与现有方法进行比较。我们首先使用六种方法计算单个基因测试的样本量,假设名义显著性水平α为0.05,功率为80%。然后,在错误发现率(FDR)为0.05和0.10的情况下,我们计算了测试多个基因的样本量。通过模拟研究,估计了六种方法估计样本量对应的差异基因表达分析的经验功率和真实预后基因。使用从对数变换和基于wald的测试中导出的样本大小公式,与其他方法相比,我们观察到更小的样本属性,同时在所有设置中保持接近或高于80%的标称功率。此外,在RNA-seq实验设计中,基于Wald检验的样本量计算方法更容易计算,速度更快。
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引用次数: 3
Bayesian Regression Analysis of Correlates of Modern ContraceptiveMethod Usage: A Case Study in Hawassa City, Ethiopia 现代避孕方法使用相关性的贝叶斯回归分析——以埃塞俄比亚哈瓦萨市为例
Pub Date : 2017-01-09 DOI: 10.4172/2155-6180.1000330
G. Kiros
Despite widespread adoption of family planning in the developing world contraceptive use is still very low in sub-Saharan Africa including Ethiopia and in other regions. The general objective of this study was identifying the socioeconomic factors of modern contraceptive methods usage among married women of reproductive ages (15-49 years old) in Hawassa city. From a total 990 sampled married women about 57.9% (573) were modern contraception methods users. Bayesian logistic regression procedure was adopted to make inference about the parameters of a logistic regression model. The purpose of this method is generating the posterior distribution of the unknown parameters given both the data and some prior density for the unknown parameters. Bayesian inference for logistic regression models is derived applying a Markov Chain Monte Carlo algorithm to simulate from the joint posterior distribution of the regression and the link parameters.
尽管发展中国家普遍采用计划生育,但包括埃塞俄比亚在内的撒哈拉以南非洲和其他地区的避孕药具使用率仍然很低。本研究的总体目标是确定哈瓦萨市育龄(15-49岁)已婚妇女使用现代避孕方法的社会经济因素。在990名已婚妇女中,约57.9%(573人)是现代避孕方法的使用者。采用贝叶斯逻辑回归程序对逻辑回归模型的参数进行推断。该方法的目的是在给定数据和未知参数的一些先验密度的情况下,生成未知参数的后验分布。应用马尔可夫链蒙特卡罗算法,从回归的联合后验分布和链路参数出发,推导了逻辑回归模型的贝叶斯推理。
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引用次数: 0
Fast Computation of Significance Threshold in QTL Mapping of DynamicQuantitative Traits 动态数量性状QTL定位中显著性阈值的快速计算
Pub Date : 2017-01-09 DOI: 10.4172/2155-6180.1000329
Nating Wang, H. Tian, Yongci Li, R. Wu, Jiangtao Luo, Zhong Wang
Functional Mapping is a popular statistical method in QTL mapping studies for longitudinal data. The threshold for declaring statistical significance of a QTL is commonly obtained through permutation tests, which can be time consuming. To improve the computational efficiency of a permutation test of mixture models used in Functional Mapping, we first quantified the correlation between QTL and longitudinal data, using a curve clustering method. Then, the QTLs which are highly correlated with the outcome were computed in the improved permutation tests. As a result, it reduces the amount of computation in permutation tests and speeds up the computation for Functional Mapping analysis. Simulation studies and real data analysis were conducted to demonstrate that the proposed approach can greatly improve the computational efficiency of QTL mapping without loss of accuracy.
在纵向数据的QTL定位研究中,功能定位是一种流行的统计方法。声明QTL统计显著性的阈值通常是通过排列测试获得的,这可能是耗时的。为了提高函数映射中使用的混合模型排列检验的计算效率,我们首先使用曲线聚类方法量化了QTL和纵向数据之间的相关性。然后,在改进的排列检验中计算与结果高度相关的QTL。因此,它减少了排列测试中的计算量,并加快了函数映射分析的计算速度。仿真研究和实际数据分析表明,该方法可以在不损失精度的情况下大大提高QTL定位的计算效率。
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引用次数: 2
Body Image and Media 身体形象与媒体
Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000368
N. Khan
A portion of youthful females may acknowledge unpredictable dietary patterns because of shameful problems about their body shape or weight, others utilize sustenance to comfort themselves as far as unforgiving conditions in their social or instructive lives. Different components can bring about these issues. This is on the grounds that specific perspectives are solid in one's choice to eat certain foodstuffs. Such solid components incorporate companion weight, family standards, social practices, accessibility of various foodstuffs, and desires.
一部分年轻女性可能会因为她们的身材或体重问题而承认不可预测的饮食模式,其他人则利用食物来安慰自己,因为他们的社会或教育生活中存在着不可原谅的条件。不同的组件会带来这些问题。这是基于一个人选择吃某些食物的特定观点是坚实的。这些坚实的组成部分包括同伴体重、家庭标准、社会习俗、各种食物的可及性和欲望。
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引用次数: 3
Human and Hummingbird Hemoglobin Concentrations and MetabolicRhythms at Altitude Determined with Statistical Modeling 人类和蜂鸟血红蛋白浓度和代谢节律在海拔与统计模型确定
Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000373
C. Qualls, C. Witt, Nicholas R. Wilson, Sebastian Restrepo Cruz, Emil Bautista, O. Appenzeller
Hummingbirds show remarkable adaptation to high altitude hypoxia whereas humans are imperfectly adapted to high altitude living. Here we compare hemoglobin levels and metabolism derived from growth rhythms in hummingbirds and humans. To compare growth rhythms, we analyzed growth intervals in hummingbird tail feathers and human growing tissues such as hair. We find that hemoglobin levels were higher in hummingbirds (P<0.001) than in humans, but the influence of altitude on hemoglobin was more pronounced in humans (slope, steeper with increasing altitude, P<0.001), and levels for both taxa converge at extreme elevations. The power spectra from growth intervals in growing tissues which reflect metabolism in both species, were not different (low frequency/high frequency ratios (LF/HF) in the two species) P>0.22 NS. In a comparison among hummingbird species, we found no evidence that metabolic demands (based on power spectra derived from growth intervals) changed with increasing altitude, even while body mass increased significantly (P>0.02). Our index of hummingbird metabolism (spectral LF/HF ratio) was consistent with estimates based on allometric conversion of mass for humans. These results support the notion that hummingbird hemoglobin levels and metabolism are useful models for biologically adaptive strategies to life at high altitude. Humans and hummingbirds exhibit convergent phenotypes for hemoglobin concentration at extreme altitudes. However, whereas human health suffers above 2500 m, hummingbirds are evolutionarily successful and physiologically robust at very high altitudes. Such different outcomes may be in part due to ancient versus recent high altitude colonization, but may also reflect greater altitude-specialization of hummingbird species, fundamental differences between avian and mammalian respiratory systems, or the very different demands of thermoregulation in hummingbirds versus humans.
蜂鸟对高海拔缺氧表现出显著的适应性,而人类对高海拔生活的适应并不完全。在这里,我们比较了蜂鸟和人类的血红蛋白水平和新陈代谢。为了比较生长节律,我们分析了蜂鸟尾羽和人类毛发等生长组织的生长间隔。我们发现蜂鸟的血红蛋白水平更高(P0.22 NS)。在蜂鸟物种间的比较中,我们没有发现代谢需求(基于生长间隔的功率谱)随海拔升高而变化的证据,即使在体重显著增加的情况下(P>0.02)。我们的蜂鸟代谢指数(光谱LF/HF比值)与基于人类异速代谢转化的估计一致。这些结果支持了蜂鸟血红蛋白水平和新陈代谢是高海拔生物适应策略的有用模型。人类和蜂鸟在极端海拔地区的血红蛋白浓度表现出趋同的表型。然而,人类健康在2500米以上受到损害,而蜂鸟在非常高的海拔上进化成功,生理健壮。这种不同的结果可能部分是由于古代和最近的高海拔定居,但也可能反映了蜂鸟物种更大的海拔专业化,鸟类和哺乳动物呼吸系统之间的根本差异,或者蜂鸟与人类对体温调节的需求非常不同。
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引用次数: 3
Spatial Autocorrelation in Voting Turnout 投票率的空间自相关
Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000376
Mahdi-Salim Saib
The presence of spatial autocorrelation in the data can yield biased or inconsistent point estimates when Ordinary Least Squares (OLS) model is used inappropriately. Therefore, in this paper we try to assess the fit of the model taking into account the autocorrelation in analyze of voting behavior in the 2007 French Presidential Elections and the 2010 French Regional Elections. We find that the voter turnout in the Il de France region is spatially structured and that the Simultaneous Auto-Regressive (SAR) model clearly improves the quality of adjustment compared with the OLS model for the both elections.
当不恰当地使用普通最小二乘(OLS)模型时,数据中空间自相关的存在会产生偏差或不一致的点估计。因此,本文在分析2007年法国总统选举和2010年法国大区选举的投票行为时,试图考虑自相关来评估模型的拟合性。我们发现,法国大区的选民投票率具有空间结构,同时自回归(SAR)模型与OLS模型相比,明显提高了两次选举的调整质量。
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引用次数: 5
Dose Finding for Drug Combination in Early Cancer Phase I Trials using Conditional Continual Reassessment Method. 使用条件连续重新评估方法寻找早期癌症I期临床试验中药物联合的剂量。
Pub Date : 2017-01-01 Epub Date: 2017-11-27 DOI: 10.4172/2155-6180.1000381
Márcio Augusto Diniz, Quanlin-Li, Mourad Tighiouart

We describe a dose escalation algorithm for drug combinations in cancer phase I clinical trials. Parametric models for describing the association between the doses and the probability of dose limiting toxicity are used assuming univariate monotonicity of the dose-toxicity relationship. Trial design proceeds using the continual reassessment method, where at each stage of the trial, we seek the dose of one agent with estimated probability of toxicity closest to a target probability of toxicity given the current dose of the other agent. A Bayes estimate of the maximum tolerated dose (MTD) curve is proposed at the conclusion of the trial for continuous doses or a set of MTDs is determined in the case of discrete dose levels. We evaluate design operating characteristics in terms of safety of the trial and percent of dose recommendation at dose combination neighborhoods around the true MTD under various model generated scenarios and misspecification. The method is further assessed for varying algorithms enrolling cohorts of two and three patients receiving different doses and compared to previous approaches such as escalation with overdose control and two-dimensional design.

我们描述了癌症I期临床试验中药物组合的剂量递增算法。假设剂量-毒性关系的单变量单调性,使用参数模型来描述剂量和剂量限制毒性概率之间的关系。试验设计使用持续重新评估方法进行,在试验的每个阶段,我们寻求一种药物的剂量,其估计毒性概率最接近给定另一种药物当前剂量的目标毒性概率。对于连续剂量,在试验结束时提出最大耐受剂量(MTD)曲线的贝叶斯估计,对于离散剂量水平,则确定一组最大耐受剂量。我们根据试验的安全性和在各种模型生成情景和错误规范下,在真实MTD附近的剂量组合区域推荐剂量的百分比来评估设计操作特性。该方法进一步评估了不同的算法,纳入了接受不同剂量的2名和3名患者的队列,并与之前的方法(如过量控制的升级和二维设计)进行了比较。
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引用次数: 10
Determination of Association between Duration of Labour and Some Social Status Using Chi-Square Distribution (χ 2 ) 用卡方分布确定劳动时间与某些社会地位的关系(χ 2)
Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000372
O. Peter, Iornongo Ag
A sample of two hundred and seventy (270) women based on child delivery were randomly selected from General Hospital North-Bank Makurdi, Benue State. Data was analyzed using Chi-square (χ2) test of independence using SPSS Version 20. The result shows that Multiparous are most likely to have shorter labour durations that is between 0-4 hours than Primiparous women and both have equal chance of having prolonged duration of labour in Makurdi local government area of Benue State at 29.6% and 15.9%, 8.9% and 8.9% respectively. Multiparous women are most likely to present at the second stage of labour with a total of 30.0% than Primiparous women. Most Primiparous women with a total of 27.8% are most likely to present at first stage of labour. There is no association between Duration of labour and Social Status of women in Makurdi local government area of Benue State. However, the duration of labour is significantly associated with the stage of presentation of delivering women hence the higher the parity the shorter the duration of labour.
从贝努埃州马库尔迪北岸总医院随机抽取了270名分娩妇女的样本。使用SPSS Version 20对数据进行χ2独立性检验。结果显示,在贝努埃州马库尔迪地方政府地区,多产妇女比初产妇女的分娩时间更短,在0-4小时之间,两者的分娩时间延长的机会相同,分别为29.6%和15.9%,8.9%和8.9%。多胎妇女最有可能在产程第二阶段出现,比初产妇女占30.0%。大多数初产妇女最有可能在分娩的第一阶段出现,总数为27.8%。贝努埃州马库尔迪地方政府地区妇女的劳动时间与社会地位之间没有联系。但是,分娩持续时间与产妇的分娩阶段有很大关系,因此胎次越高,分娩持续时间越短。
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引用次数: 0
Tooth Growth in Ancient and Modern Times Inferred from Perikymata Growth Intervals; Modeled Statistically 由外突生长时间推断古今牙齿生长统计建模
Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000380
C. Qualls, M. A. Costa, M. Paffett, O. Appenzeller
Tooth growth is essential to health and survival. In humans the growth rate can be inferred from the width of perikymata growth intervals. We hypothesized that in ancient times teeth grew faster than in modern humans. We measured the intervals between perikymata ridges on the surfaces of teeth and in thin sections of molars (which we used as standards) in ancient, prehistoric and modern humans. We compared statistically the results from ancient and modern specimens and assessed the impact of dietary factors and sociality on tooth growth. We found that ancient teeth grew faster than modern teeth (wider intervals) because of environmental, nutritional and life style influences. This apparently conferred evolutionary advantages for human survival. Our results gleaned from combining measurements of sections of teeth with modeling of web-available images suggest that life styles of modern humans have lead to smaller teeth.
牙齿的生长对健康和生存至关重要。在人类中,生长速度可以从周围突起生长间隔的宽度推断出来。我们假设古代人类的牙齿比现代人长得快。我们测量了古代、史前和现代人类牙齿表面和臼齿薄片之间的间隙(我们以此为标准)。我们统计比较了古代和现代标本的结果,并评估了饮食因素和社会对牙齿生长的影响。我们发现,由于环境、营养和生活方式的影响,古代牙齿比现代牙齿生长得更快(间隔更宽)。这显然赋予了人类生存的进化优势。我们将牙齿切片的测量结果与网络上可获得的图像建模相结合,得出的结果表明,现代人的生活方式导致了牙齿变小。
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引用次数: 1
Audio-Visual Person Recognition Using Deep Convolutional Neural Networks 基于深度卷积神经网络的视听人物识别
Pub Date : 2017-01-01 DOI: 10.4172/2155-6180.1000377
Sagar Vegad, H. Patel, H. Zhuang, M. Naik
Protection of data integrity and person identity has been an active research area for many years. Among the techniques investigated, developing multi-modal recognition systems using audio and face signals for people authentication holds a promising future due to its ease of use. A challenge in developing such a multi-modal recognition system is to improve its reliability for a practical application. In this paper, an efficient audio-visual bimodal recognition system which uses Deep Convolution Neural Networks (CNNs) as a primary model architecture. First, two separate Deep CNN models are trained with the help of audio and facial features, respectively. The outputs of these CNN models are then combined/fused to predict the identity of the subject. Implementation details with regard to data fusion are discussed in a great length in the paper. Through experimental verification, the proposed bimodal fusion approach is superior in accuracy performance when compared with any single modal recognition systems and with published results using the same data-set.
多年来,数据完整性和个人身份保护一直是一个活跃的研究领域。在研究的技术中,开发使用音频和面部信号进行身份验证的多模态识别系统因其易于使用而具有广阔的前景。开发这种多模态识别系统的一个挑战是如何提高其实际应用的可靠性。本文提出了一种以深度卷积神经网络(cnn)为主要模型结构的高效视听双峰识别系统。首先,分别在音频和面部特征的帮助下训练两个独立的Deep CNN模型。然后将这些CNN模型的输出组合/融合以预测主体的身份。文中对数据融合的实现细节作了较长的讨论。通过实验验证,与单模态识别系统和使用相同数据集的已发表结果相比,所提出的双模态融合方法具有更高的精度。
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引用次数: 7
期刊
Journal of biometrics & biostatistics
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