非一致性水文频率计算的基因途径Ⅱ:水文基因诊断系统与非一致性常规矩基因方法

非一致性水文频率分析是变化环境下工程水文计算需要解决的主要问题之一.本文从随机水文序列组成的角度,将不同时间尺度下的非一致性水文现象概化为具有遗传、变异与进化特性或规律的水文过程,据此借鉴生物基因理论提出水文基因的概念,并定义常规矩基因为水文序列的各阶原点矩和中心矩.为了识别与检验水文基因的各组成成分,创建了水文基因诊断系统.为了阐述水文基因的遗传、变异与进化原理,以P-Ⅲ分布为例详细描述了常规矩基因的构建与表达过程.以澜沧江流域允景洪站年最小1月流量序列为例,对上述基于常规矩基因的非一致性水文频率计算方法进行了可行性和实用性验证.结果表明: 该方法能以水文基因变异识别为基础,揭示非一致性水文序列的演变规律,不仅为变化环境下工程水文计算提供了新的研究途径,也能为水安全评价提供重要的参考依据.     

非一致性水文频率计算的基因途径Ⅰ:水文基因遗传、变异和进化原理

随机水文过程受到随机性和确定性因素的综合影响,其时间序列不仅具有反映遗传特性的纯随机成分,还含有反映变异特性的确定性跳跃、趋势、周期成分和随机性相依成分,使得随机水文过程表现出复杂的变化形态和演变规律.为了对上述复杂的变化形态和演变规律进行统一认识,本文从随机过程模拟和时间序列分析两个角度描述了非一致性水文序列的遗传和变异特性或规律,同时对非一致性水文频率计算途径进行比较,说明非一致性研究面临的主要问题.在此基础上,本文借鉴生物基因概念来定义水文基因,并分别利用常规矩、权函数矩、概率权重矩、线性矩等描述水文基因的构建和表达过程;同时定义跳跃、趋势、周期、相依和纯随机成分为构成水文基因的5种水文碱基,综合考虑非一致性水文序列的遗传成分和变异成分,并阐述其遗传、变异和进化原理,以揭示水文要素概率分布遗传、变异和进化的演变规律.     

水文跳跃变异综合加权识别方法——以澜沧江下游戛旧水文站径流序列为例

跳跃变异是全球气候变化背景下水文过程发生剧烈变异的重要表现形式,其准确识别对认识水文过程发生的变化及开展实际水文水资源工作具有重要意义.针对目前传统方法在样本两端有时检验结果不可靠、多种方法检验结果常常不一致等问题,本文通过对常用的12种变异点检验方法对比研究,基于赋权方式提出了水文跳跃变异综合加权识别方法,并利用Monte-Carlo统计试验验证了该方法的可靠性.结果表明: 12种跳跃变异检验方法的效率受变异点前变差系数(Cv)、变异点前偏态系数(Cs)、均值变幅系数、Cv变幅系数、Cs变幅系数等因素的影响较大,但与序列均值无明显关系.以各方法的性能差异为基础,基于统计试验结果对各检验方法赋予权重.其中,滑动秩和检验法和滑动游程检验法的权重最高,RS检验法的权重最低.通过赋权方式,可以在各方法检测结果不一致时选取综合权重最大的变异点作为最终结果.将该方法应用于澜沧江下游戛旧年径流极大值(1日、3日、5日、7日、1月)序列进行分析,结果显示各个序列均在2004年发生了明显跳跃变异,且与该流域水文过程变化、水利工程建设等物理成因十分吻合,验证了该方法的合理性和可靠性.     

变异条件下淮河流域生态径流变化特征及驱动因子

基于淮河流域7个水文站点1956—2016年逐日径流量和72个雨量站点1960—2016的逐日降水量数据,利用Pettitt变异点检测、生态赤字和生态剩余等生态径流指标,定量分析淮河流域水文变异特征,根据生物多样性指标和水文变异指数间的关系,分析该流域水文变异的生态效应,利用位置、尺度、形状的广义可加模型(Generalized Additive Models for Location, Scale and Shape,GAMLSS)理论框架量化气候因子对生态径流变化的贡献。研究表明:(1)水文变异后生态剩余减少,生态赤字增多,干流流量历时曲线比支流下移更明显;年生态剩余/赤字与面降水距平变化一致,水利工程调蓄作用是夏季生态径流与降水距平相关性差的主要原因;(2)除冬季外,淮河流域年、季尺度生态赤字(生态剩余)逐年增加(减小),春季增加最为明显。尽管冬季生态剩余比其他季节高,但生态剩余整体减小,21世纪干流生态剩余达最低,香农指数表明淮河流域生物多样性逐年下降。生态径流指标与水文改变指标(Indicators of Hydrologic Alteration,IHA)指标相关达0.45...     

结合基因功能分类体系Gene Ontology筛选聚类特征基因

使用两套基因表达谱数据,按各基因的表达值方差,选择表达变异基因对样本聚类,发现一般使用方差较大的前10％的基因作为特征基因,就可以较好地对疾病样本聚类。对不同的疾病,包含聚类信息的特征基因有不同的分布特点。在此基础上,结合基因功能分类体系(Gene Ontology,GO),进一步筛选聚类的特征基因。通过检验在Gene Ontology中的每个功能类中的表达变异基因是否非随机地聚集,寻找疾病相关功能类,再根据相关功能类中的表达变异基因进行聚类分析。实验结果显示：结合基因功能体系进一步筛选表达变异基因作为聚类特征基因,可以保持或提高聚类准确性,并使得聚类结果具有明确的生物学意义。另外,发现了一些可能和淋巴瘤和白血病相关的基因。     

融合位置特征与序列进化信息的磷酸化位点预测（英文）

磷酸化是蛋白质翻译后的主要修饰,可分为激酶特异性和非激酶特异性两种类型.以非激酶特异性磷酸化位点Dou数据集为基础,本文发展了一种基于位置的卡方差表特征χ~2-pos,融合伪氨基酸序列进化信息PsePSSM表征序列,构建正负样本均衡的支持向量机分类器,S,T,Y独立测试Matthew相关系数、ROC曲线下面积分及准确率分别达到了(0.59、0.87、79.74%),(0.55、0.85、77.68%)和(0.50、0.81、75.22%),明显优于文献报道结果.χ~2-pos、PsePSSM两种特征的融合在蛋白质磷酸化位点预测中有广泛应用前景.     

基于生态系统受扰动程度评价的白洋淀生态需水研究

水是湿地生态系统最重要的影响因子,生态需水核算是对湿地进行生态保护,恢复重建的前提与基础.提出一种基于生态系统受扰动程度评价的适宜生态需水量计算方法.首先根据湿地水面面积变化率最大时对应的关键水位构建初始生态水位方案并将其离散得到一系列离散值;然后应用Mann-Kendall(M-K)法分析历史水位时间序列,找出水位发生突变前自然条件下的水位状态;最后对不同情景水位方案与自然水位状态的差异程度进行修正水文指数(APPFD)评价,确定生态系统受扰动程度在可接受范围之内的多个生态水位方案,进而确定相对应的生态需水量方案.将该方法应用于白洋淀湿地得出了7种可接受的生态水位方案,其中汛期的适宜生态水位在8.31-10.62 m之间,非汛期的适宜生态水位在7.51-9.60 m之间,全年的适宜生态需水量在3.10×108-6.47×l08m3之间.该方法能够为实际的水资源管理和分配提供多种备选方案,有较强的实用性和可操作性.     

非等试验设计胚乳品质性状的遗传分析方法

根据朱军(1996)提出的包括基因型×环境互作的胚乳品质性状三倍体遗传模型,运用蒙特卡罗模拟证明,以混合线性模型统计分析的MINQUE法,对非等试验设计获得的实验数据进行数量遗传分析是可行的.蒙特卡罗模拟结果表明在样本群体大小基本一致的条件下,采用相等试验设计或非等试验设计所估算的遗传参数的偏差(Blas)和功效值(Power)没有明显差异,表明以非等试验设计获得的非平衡数据也可用来进行遗传分析,估算上述遗传模型中的各项遗传方差分量和协方差分量,并且可以采用朱军(1993)提出的AUP法来预测遗传模型中的各项遗传效应值.     

融合位置特征与序列进化信息的磷酸化位点预测

磷酸化是蛋白质翻译后的主要修饰,可分为激酶特异性和非激酶特异性两种类型．以非激酶特异性磷酸化位点Dou数据集为基础,本文发展了一种基于位置的卡方差表特征χ²-pos,融合伪氨基酸序列进化信息PsePSSM表征序列,构建正负样本均衡的支持向量机分类器,S, T, Y独立测试Matthew相关系数、ROC曲线下面积分及准确率分别达到了(0.59、0.87、79.74%),(0.55、0.85、77.68%)和(0.50、0.81、75.22%),明显优于文献报道结果． χ²-pos、PsePSSM两种特征的融合在蛋白质磷酸化位点预测中有广泛应用前景．     

黑麦特异重复序列pSc119.1在姊妹T1RS·1BL易位系中的变异

根据公布的黑麦特异重复序列pSc119.1设计特异引物, 分别对两套姊妹T1RS·1BL易位系川农12(CN12)、川农17(CN17)、川农18(CN18)和96Ⅰ176-1、96Ⅰ176-3的基因组DNA进行扩增。从CN12、CN17、CN18的基因组中都能扩增出目的片段, 在96Ⅰ176-1的基因组中, 除目的片段外, 还扩增出了一条非目的片段, 但在96Ⅰ176-3的基因组中没有扩增出产物。Southern blot分析表明, pSc119.1序列并未从96Ⅰ176-3的基因组中消失。将CN12、CN17、CN18的目的片段回收克隆后, 对每个片段各随机挑取10个克隆进行测序, pSc119.1序列在3个品种中都发生了变异, 且在CN18中的变异程度最大。所测的序列多数与原序列达94%和95%的相似性, 在这些序列中, 碱基的改变具有一定的规律, 即多数为转换, 少数为颠换, 且变异碱基和变异位置具有较高的一致性。远缘杂交后代的进化可能是一个持续过程, 姊妹系内的株系之间某些性状存在差异, 这些差异很可能与重复序列的变异有关, 这为后生遗传效应机制的研究提供了有用的材料。     

基于相关系数的水文相依性变异分级方法——以自回归模型为例

水文过程演变存在时间相依性,含有相依成分的水文序列无法满足水文计算中的一致性假设,给水问题研究带来诸多困难.针对水文序列相依性变异这一现象,以自相关模型为例,提出基于相关系数的水文相依性变异分级方法.该方法通过计算相依成分与原序列之间的相关系数,并选取合理的相关系数阈值,将相依性变异程度分为无变异、弱变异、中变异、强变异、巨变异.通过推导相关系数与序列各阶自相关系数之间的公式,说明相关系数主要取决于1阶到p阶自相关系数的大小,从而阐明分级方法的理论基础.以一阶和二阶自回归模型为例,利用统计试验验证了公式的合理性,并说明了相关系数和自相关系数的联系.将所提分级方法应用于3个实测径流序列进行分析,结果显示水文过程常常存在相依性与随机性并存的现象.     

Variations in polymer fitness at elevated mutation rates

Two series expressions were obtained that give the first and second order rates of change in population fitness during competitive replication at elevated mutation rates. At their zeroerror limit, the respective power series reduces to the second (Fisher’s theorem) and third moments of the fitness distribution. The first series maximized the variation in mean polymer fitness, for a given amount of population covariance. From experimental results reported by Spiegelman’s group on evolutionin vitro among Qβ RNA variants, it was demonstrated: (i) terms in the (second) series fall-off at a rate broadly equal to the replicase error (ε≅10⁻⁴); (ii) the rate of change in mean RNA fitness (polymer formation rate constant) corresponds to the variance in fitness; and (iii) agreement exists between second order rate changes in fitness and the third moment (skewness) regression line, extending over 20 successive replication reactions. The impact of these findings on the standard model of evolution has been discussed.     

Aging, regularity and variability in maximum isometric moments

This study examined the variability and regularity of maximum isometric moment production of the plantar flexors in young and old subjects. It was hypothesized that in the development of maximum isometric moments there would be greater regularity in the moment profiles for older subjects compared with young subjects, due to the reduced number of motor units present in elderly muscle. Two groups of subjects produced three maximal isometric plantar flexions (young: n=11, mean age 23.8+/-2.8 years, mean mass 81.2+/-10.4 kg, mean height 1.78+/-0.05 m; elderly: n=13, mean age 74.0+/-3.3 years, mean mass 78.5+/-3.4 kg, mean height 1.73+/-0.05 m). The plateau of the moment-time curve was analyzed for each trial. A repeat measures analysis of variance showed the young subjects produced statistically greater peak plantar flexion moments than the elderly subjects, but similar coefficients of variation. Signal regularity was determined by computing the signal's approximate entropy, which demonstrated that the older group had greater regularity in their generation of moment profiles. The hypothesis was accepted, with a potential explanation for this increased regularity in old age being the reduced number of motor units to coordinate.     

The effects of climate change on density‐dependent population dynamics of aquatic invertebrates

Global climate change has the potential to alter aquatic communities through changes in evapotranspiration and increased variability in precipitation. We used aquatic mesocosms to test the impacts of variable precipitation on population dynamics of common mosquito (Culicidae) and midge (Chironomidae) larvae that inhabit vernal pools. In a mixed deciduous forest in northern Vermont, USA, we orthogonally crossed seven levels of mean water level (increased rainfall) with seven levels of water level coefficient of variation (more variable rainfall) to simulate a broad array of climate change scenarios in 49 experimental mesocosms. The average abundance of Culicidae was highest at low water levels, whereas the average abundance of Chironomidae was highest at higher water levels and low variability in water level. Treatments and environmental and spatial covariates collectively explained 49% of the variance in mean abundance. For both taxa, we fit hierarchical Bayesian models to each 16‐week time series to estimate the parameters in a Gompertz logistic equation of population growth with density dependence. We found that Culicidae population growth rate increased with decreasing water levels and that 87% of the variance in Chironomidae density dependence could be explained by treatment. Collectively, these results suggest that climate change can alter abundances aquatic invertebrate taxa but not necessarily through the same mechanism on all populations. In the case of Culicidae the abundance is affected by changes in growth rate, and in Chironomidae by changes in the strength of density dependence.     

Using a mixed effects model to estimate geographic variation in cancer rates

Commonly used methods for depicting geographic variation in cancer rates are based on rankings. They identify where the rates are high and low but do not indicate the magnitude of the rates nor their variability. Yet such measures of variability may be useful in suggesting which types of cancer warrant further analytic studies of localized risk factors. We consider a mixed effects model in which the logarithm of the mean Poisson rate is additive in fixed stratum effects (e.g., age effects) and in logarithms of random relative risk effects associated with geographic areas. These random effects are assumed to follow a gamma distribution with unit mean and variance 1/alpha, similar to Clayton and Kaldor (1987, Biometrics 43, 671-681). We present maximum likelihood and method-of-moments estimates with standard errors for inference on alpha -1/2, the relative risk standard deviation (RRSD). The moment estimates rely on only the first two moments of the Poisson and gamma distributions but have larger standard errors than the maximum likelihood estimates. We compare these estimates with other measures of variability. Several examples suggest that the RRSD estimates have advantages compared to other measures of variability.     

Foraging juncos: interaction of reward mean and variability

Recent stochastic theories of feeding strategy propose that a risk-averse forager will trade off increases in reward variability against increases in average reward. We show that two models of risk-aversion (variance discounting and the z-score model) imply different forms for this interaction of mean and variability. Variance discounting suggests constant risk-aversion, since the effect of reward variance on expected fitness is assumed to be independent of the mean. The z-score model suggests decreasing risk-aversion, since the effect of a given level of reward variance on expected fitness is assumed to decrease as the mean increases. We report two series of experiments with dark-eyed juncos (Junco hyemalis). Each series investigated the mean-variability trade-off under physiological conditions promoting risk-aversion; reward sizes were generally greater in the second series. The results clearly indicate a trade-off, but within a series the data do not discriminate between the two models' predictions. Comparing the two series suggests that the juncos' level of aversion to reward variability decreases after an overall increment in environmental profitability.     

Differences in lower limb transverse plane joint moments during gait when expressed in two alternative reference frames

When comparing previous studies that have measured the three-dimensional moments acting about the lower limb joints (either external moments or opposing internal joint moments) during able-bodied adult gait, significant variation is apparent in the profiles of the reported transverse plane moments. This variation cannot be explained on the basis of adopted convention (i.e. external versus internal joint moment) or inherent variability in gait strategies. The aim of the current study was to determine whether in fact the frame in which moments are expressed has a dominant effect upon transverse plane moments and thus provides a valid explanation for the observed inconsistency in the literature. Kinematic and ground reaction force data were acquired from nine able-bodied adult subjects walking at a self-selected speed. Three-dimensional hip, knee and ankle joint moments during gait were calculated using a standard inverse dynamics approach. In addition to calculating internal joint moments, the components of the external moment occurring in the transverse plane at each of the lower limb joints were calculated to determine their independent effects. All moments were expressed in both the laboratory frame (LF) as well as the anatomical frame (AF) of the distal segment. With the exception of the ankle rotation moment in the foot AF, lower limb transverse plane joint moments during gait were found to display characteristic profiles that were consistent across subjects. Furthermore, lower limb transverse plane joint moments during gait differed when expressed in the distal segment AF compared to the LF. At the hip, the two alternative reference frames produced near reciprocal joint moment profiles. The components of the external moment revealed that the external ground reaction force moment was primarily responsible for this result. Lower limb transverse plane joint moments during gait were therefore found to be highly sensitive to a change in reference frame. These findings indicate that the different transverse plane joint moment profiles during able-bodied adult gait reported in the literature are likely to be explained on this basis.     

Environmental control of vessel traits in Quercus ilex under Mediterranean climate: relating xylem anatomy to function

Time series of tree-ring anatomical features are important to understand the functional role of xylem plasticity over the life span of trees, and thus to reconstruct past ecological and climatic conditions. Holm oak (Quercus ilex L.) is a drought-tolerant tree widely distributed in the Mediterranean Basin. Chronologies of tree-ring width (TRW), vessel lumen area [maximum (MAX) and mean (MVA)] and vessel density (VD) were developed for the period 1942–2001. Each ring was divided into three sections to compare the intra-annual variation of vessel features with the climate conditions during the growing season. The common variability of tree-growth and vessel features was analyzed using a principal component analysis (PCA). Vessel lumen area (MAX and MVA) and TRW loaded positively on the first axis (PC1), whereas VD from the first and second part of the ring (VD1 and VD2) loaded negatively, suggesting that these variables share a common variance. On the other hand, VD in the last third of the ring (VD3) loaded positively on second axis (PC2). PC1 showed a strong positive correlation with precipitation during the hydrological year (prior October–September) and a negative correlation with temperature in spring (April–May), while PC2 showed a negative correlation with precipitation in June. Our results showed that TRW and vessel lumen area were mainly dependent on moisture conditions along the growing season, while vessel density probably plays an important role in the balance between hydraulic conductivity and safety to embolism to better adjust the hydraulic system to water availability.