基于极大似然准则的生物序列模体的贝叶斯假设检验

针对生物信息学中序列模体的显著性检验问题,提出了一种基于极大似然准则的贝叶斯假设检验方法.将模体的显著性检验转化为多项分布的拟合优度检验问题,选取Dirichlet分布作为多项分布的先验分布并采用Newton-Raphson算法估计Dirichlet分布的超参数,使得数据的预测分布达到最大.应用贝叶斯定理得到贝叶斯因子进行模型选择,用于评价模体检验的统计显著性,这种方法克服了传统多项分布检验中构造检验统计量并计算其在零假设下确切分布的困难.选择JASPAR数据库中107个转录因子结合位点和100组随机模拟数据进行实验,采用皮尔逊积矩相关系数作为评价检验质量的一个标准,发现实验结果好于传统的模体检验的一些方法.     

Evaluation of FORS-D Analysis: A Comparison with the Statistically Significant Stem-loop Potential

The stem-loop potential of a nucleic acid segment (expressed as a FONS value), decomposes into base composition-dependent and base order-dependent components. The latter, expressed as a FORS-D value, is derived by subtracting the value of the base composition-dependent component (FORS-M) from the FONS value. FORS-D analysis is the use of FORS-D values to estimate the potential of local base order to contribute to a stem-loop structure, and it has been used to investigate the relationship between stem-loop structure and other selective pressures on genomes. In the present study, we evaluated the reliability of FORS-D analysis by comparing it with statistically significant stem-loop potential, another robust method developed by Le and Maizel for examining stem-loop structure. We found that FORS-M values calculated using 10 randomized sequences are as reliable as those calculated using 100 randomized sequences. The resulting FORS-D values have a similar trend and distribution as statistically significant stem-loop potential, implying that FORS-D analysis is as reliable as the latter in measuring the distribution of base order-dependent stem-loop potential. Since the calculation of the FORS-M values is time consuming, the integrated program Bodslp developed by us will become a convenient tool for large-scale FORS-D analysis. The results also suggest that for some purposes the online program SigStb developed by Le and Maizel may be used as an alternative tool for FORS-D analysis. C. Y. Zhang and J. F. Wei contributed equally to this paper.     

A new MSPQC for rapid growth and detection of Mycobacterium tuberculosis

Many of the deaths caused by tuberculosis (TB) in the world are due to wrong or late diagnosis. The World Health Organization (WHO) calls for better and cheaper TB tests method for this reason. In this paper, a new multi-channel series piezoelectric quartz crystal (MSPQC) sensor system was developed for rapid growth and detection of Mycobacterium tuberculosis. It is an automatic continuous monitoring system. The system was used to detect TB based on the volatile metabolic products NH(3) and CO(2) during the growth of M. tuberculosis. The metabolic products, diffusing from the medium into the KOH absorbing solution, resulted in the conductance change of the absorbing solution detected by the MSPQC sensitively. The frequency shift versus time response curves were recorded by self-developed software. Frequency detection time (FDT) corresponding to -100Hz in frequency shift value was used as a parameter to quantitatively determine M. tuberculosis H37Ra (an avirulent strain). H37Ra and 40 strains clinic positive samples were detected by the proposed system successfully. As for H37Ra, the FDT had a linear relationship with the logarithm of its initial concentration in the range of 10(2)-10(7) colony forming units (cfu)ml(-1) (R=-0.998) and the detection limit was low to 10cfuml(-1). 4% NaOH solution that can kill contaminating microorganisms and make M. tuberculosis alive was used as pretreatment reagent to provide selectivity to this method. Comparative tests were also carried out by using BACTECtrade mark MGITtrade mark 960 and conventional Lowenstein-Jensen (L-J) slants. The results showed that the proposed system was quicker than BACTECtrade mark MGITtrade mark 960 and it is also cheaper and will be widely used in TB tests in the world.     

Sampling techniques and the use of Tang's procedure in insect population dynamics studies

Some calculations were performed usingTang 's method as an aid in planning experiments for studying the population dynamics of the Jeffrey pine beetle. The population dynamics studies were aimed at detecting the importance of specific effects, e. g., tree diameter, tree height. TheTang procedure is a method of estimating the sample size required to detect effects of a given magnitude with analysis of variance tests. Using this procedure some sample calculations were performed which indicated the sample size needed, and the efficacy of different strategies of improving the results, e. g., increasing the number of trees sampled versus increasing the area of the tree sampled. The statistical parameters used in the calculations were estimated from some preliminary sampling data. Use of this procedure is recommended in insect population studies as a method of optimally planning experiments, and as a method of making precise conclusions about the significance of specific effects.     

On Fisher's Method of Combining p-Values

The problem of combining p-values from independent experiments is discussed. It is shown that Fisher's solution to the problem can be derived from a “weight-free” method that has been suggested for the purpose of ranking vector observations (Biometrics 19: 85–97, 1963). The method implies that the value p = 0.37 is a critical one: p-values below 0.37 suggest that the null hypothesis is more likely to be false, whereas p-values above 0.37 suggest that it is more likely to be true.     

循证护理对肝硬化腹水患者的疗效分析

目的:循证护理根据有价值的、可信的科学研究结果,提出问题,寻找实证,对病人采用最佳的护理模式进行护理。本文通过临床观察,旨在探讨循证护理对肝硬化腹水患者的临床疗效。方法:回顾性分析我院2009年2月到2012年6月收治的74例肝硬化腹水患者的临床资料,根据不同的护理方法将所选患者分为干预组和对照组,每组各37例。对照组患者给予常规护理,干预组患者在常规护理的基础上给予循证护理。观察两组患者的心理功能、生活能力、社交功能的改善情况,并比较两组患者的并发症发生情况及治疗的总有效率。结果:在接受不同的护理干预后,干预组患者的心理功能、生活能力、社交功能均显著优于对照组患者,差异具有统计学意义(P0.05);干预组患者的并发症发生率为5.40%,显著低于对照组患者的并发症并发率16.22%,差异显著有统计学意义(P0.01);干预组患者的总有效率为94.59%,明显高于对照组患者的总有效率83.78%,两组比较差异显著(P0.05)。结论:循证护理模式有助于肝硬化腹水患者的心理功能、生活能力、社交功能得到改善,临床效果满意,值得推广。     

2016—2018年某医院肺炎克雷伯菌的临床分布及耐药性分析

目的分析某院肺炎克雷伯菌(Klebsiella pneumoniae, KPN)的临床分布,产超广谱β-内酰胺酶(extended-spectrum β-lactamase, ESBLs)的情况以及综合耐药特点,为临床经验性选用抗生素提供参考。方法回顾性分析某院2016-2018年临床分离培养的KPN耐药数据及临床资料,菌株均采用全自动分析仪进行菌种鉴定和药敏分析。结果 3年间共检出非重复KPN 2 211株,样本分布结果显示,KPN最多的是痰液1 268株,占57.35%;脑脊液最少12株,仅占0.54%。临床科室分布来看,ICU病房分离KPN最多274株,占12.39%;乳甲外科最少5株,仅占0.23%。2 211株KPN共检出ESBLs阳性708株,检出率为32.02%。KPN对头孢唑林、头孢呋辛、头孢曲松和复方新诺明的耐药率均已超过40%,对亚胺培南、阿米卡星和美罗培南耐药率仅为5.20%。与胆汁、血液和痰液样本中KPN的耐药性相比,尿液分离株的耐药性普遍较高(P<0.05)。结论 ESBLs检出率较高,耐药情况较为严峻,并且不同样本来源菌株的耐药性有较大差异,以尿液分离株的耐药性更为严重。医院需加强对重点科室,不同样本中KPN的耐药性监测,合理使用抗生素。     

儿童及青少年甲状腺癌特点及颈淋巴结转移风险因素探讨

目的:探讨儿童及青少年甲状腺癌的临床和病理特征,分析乳头状癌组淋巴结转移的风险因素。方法:回顾性分析2003年1月至2013年12月间本院收治的儿童及青少年甲状腺癌病例资料,了解临床特征和病理特点及分析乳头状癌亚组淋巴结转移的风险因素。结果:共收集51例儿童及青少年甲状腺癌资料,49例甲状腺乳头状癌,2例甲状腺髓样癌。乳头状癌亚组淋巴结转移率达77.5%,患儿年龄与淋巴结转移相关,Logistic回归提示年龄是颈部淋巴结转移的独立风险因素(OR=1.40;95%CL=1.05,1.85;P=0.021)。随访中5例出现局部复发。结论:儿童及青少年甲状腺癌有区别于成人甲状腺癌的特殊性,积极筛查儿童甲状腺疾病、全面彻底的外科手术和制定相应的风险评估标准、积极随访是治疗该病的关键。     

Did natural selection make the Dutch taller? A cautionary note on the importance of quantification in understanding evolution

One of the main achievements of the modern synthesis is a rigorous mathematical theory for evolution by natural selection. Combining this theory with statistical models makes it possible to estimate the relevant parameters so as to quantify selection and evolution in nature. Although quantification is a sign of a mature science, statistical models are unfortunately often interpreted independently of the motivating mathematical theory. Without a link to theory, numerical results do not represent proper quantifications, because they lack the connections that designate their biological meaning. Here, we want to raise awareness and exemplify this problem by examining a recent study on natural selection in a contemporary human population. Stulp et al. (2015) concluded that natural selection may partly explain the increasing stature of the Dutch population. This conclusion was based on a qualitative assessment of the presence of selection on height. Here, we provide a quantitative interpretation of these results using standard evolutionary theory to show that natural selection has had a minuscule effect.     

Comparison of t-tests for differences in sexual dimorphism between populations

A t-test that can be used for evaluating the significance of differences in metric sexual dimorphism between populations is derived directly from mathematical considerations of the differences between distributions. It is compared with the t-test derived by Relethford and Hodges (1985), which was based upon linear regression with sex as a dummy variable. Both are determined to be mathematically equivalent, though the one derived here is more similar in form to traditional t-tests of differences and therefore may be simpler to employ. Both tests require only summary statistics for comparisons between populations and comparisons between generations within populations.