Different responses to changes in phosphorus,P, among lakes. A study of slopes in chl-a = f(P) graphs

The least squares estimator of a linear regression coefficient _L will give an overall expression for the change in with x. In fresh water ecology, however, subgroups, % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiuaSGaci% 4Aaaaa!37BE!\[P\operatorname{k}\], of a parent population may have slopes which differ from the overall slope, _L. By constructing frequency histograms for the set of angles: Arctang % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaci4uaSGaam% yAaiaadQgaaaa!38AE!\[\operatorname{S} ij\],% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaci4uaSGaam% yAaiaadQgaaaa!38AE!\[\operatorname{S} ij\]= para sa y and x% MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaaiikaiaadM% faliaadMgakiabgkHiTiaadMfaliaadQgakiaacMcacaGGVaGaaiik% aiaadIhaliaadMgakiabgkHiTiaadIhaliaadQgakiaacMcaaaa!42F0!\[(Yi - Yj)/(xi - xj)\], i < j, % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiEaSGaam% yAaOGaeyiyIKRaamiEaSGaamOAaaaa!3BAB!\[xi \ne xj\], peaks in the distribution may be identified and related to ecological phenomenon. To identify peaks we fit Gaussian distributions to the frequency histograms. For a set consisting of 142 observations of chlorophyll-a and total phosphorus (nutrient) concentrations (TP) from 16 lakes we found four Gaussian peaks corresponding to four subgroups, % MathType!MTEF!2!1!+-% feaafiart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaamiuaSGaci% 4Aaaaa!37BE!\[P\operatorname{k}\]k = 1,4. One group identified a response of chl-a to changes in TP which correspond approximately to the average slope found by least square regression (the slope was 0.49). The second group consisted of steeper response than the average (1.28). A third group showed that there is an enhanced proportion of cases where chl-a does not respond to TP (zero slope, all the three deep lakes > 10 m, included in the date set contributed to this group). The size of the last group, spanning a wide range of slopes, suggested that about 30% of the inter annual changes in chl-a is unrelated to TP. The results are compared to result obtained by simple least squares regression and to the Theil non-parametric slope estimator.     

Statistical torsion angle potential energy functions for protein structure modeling: A bicubic interpolation approach

A set of grid type knowledge‐based energy functions is introduced for ?–χ₁, ψ–χ₁, ?–ψ, and χ₁–χ₂ torsion angle combinations. Boltzmann distribution is assumed for the torsion angle populations from protein X‐ray structures, and the functions are named as statistical torsion angle potential energy functions. The grid points around periodic boundaries are duplicated to force periodicity, and the remedy relieves the derivative discontinuity problem. The devised functions rapidly improve the quality of model structures. The potential bias in the functions and the usefulness of additional secondary structure information are also investigated. The proposed guiding functions are expected to facilitate protein structure modeling, such as protein structure prediction, protein design, and structure refinement. Proteins 2013. Proteins 2013; 81:1156–1165. © 2013 Wiley Periodicals, Inc.     

基于GIS的浙北近海海域生态系统健康评价

在浙江省北部地区经济高速发展,科学高效利用海洋资源的同时,也不可避免的对浙北近海海域的生态系统造成一定的威胁。为了降低涉海工程对海洋生态环境可能造成的不利影响,通过分析浙江省北部海域高浊度、复杂水体等特点,利用层次分析法从水环境、沉积环境和海洋生物多样性构建了浙北近海海域生态系统评价指标体系,采用熵权法确定了相关因子的权重。在此基础上,综合GIS空间分析方法、数学模型,对2009年至2012年浙江省北部海域进行了实证研究。结果表明:(1)浙江省北部近海海域生态系统整体上处于不健康状态。含量较高的无机氮和磷酸盐及较低的海洋初级生产力是影响其环境质量的主要因素。(2)浙北近海海域生态系统主要薄弱区域与人类活动格局基本一致,由此推断,人类活动是影响浙北海域生态系统健康状态的主要因素。总体上,从2009至2012年浙北近海海域生态系统健康呈现逐年恶化的趋势。     

An evaluation of transferability of ecological niche models

Ecological niche modeling (ENM) is used widely to study species’ geographic distributions. ENM applications frequently involve transferring models calibrated with environmental data from one region to other regions or times that may include novel environmental conditions. When novel conditions are present, transferability implies extrapolation, whereas, in absence of such conditions, transferability is an interpolation step only. We evaluated transferability of models produced using 11 ENM algorithms from the perspective of interpolation and extrapolation in a virtual species framework. We defined fundamental niches and potential distributions of 16 virtual species distributed across Eurasia. To simulate real situations of incomplete understanding of species’ distribution or existing fundamental niche (environmental conditions suitable for the species contained in the study area; N* _F ), we divided Eurasia into six regions and used 1–5 regions for model calibration and the rest for model evaluation. The models produced with the 11 ENM algorithms were evaluated in environmental space, to complement the traditional geographic evaluation of models. None of the algorithms accurately estimated the existing fundamental niche (N* _F ) given one region in calibration, and model evaluation scores decreased as the novelty of the environments in the evaluation regions increased. Thus, we recommend quantifying environmental similarity between calibration and transfer regions prior to model transfer, providing an avenue for assessing uncertainty of model transferability. Different algorithms had different sensitivity to completeness of knowledge of N* _F , with implications for algorithm selection. If the goal is to reconstruct fundamental niches, users should choose algorithms with limited extrapolation when N* _F is well known, or choose algorithms with increased extrapolation when N* _F is poorly known. Our assessment can inform applications of ecological niche modeling transference to anticipate species invasions into novel areas, disease emergence in new regions, and forecasts of species distributions under future climate conditions.     

使用线性微分方程构建初步的乳腺癌转移相关基因网络模型

随着基因芯片的技术的推广,越来越多的表达数据需要被处理和分析．利用这些表达数据提取基因调控矩阵从而构建基因网络是一个重要的问题．通过线性微分方程模型可以初步构建基因网络,了解网络结构,提取最显著的信息．然而由于分子生物学的条件限制或者数据来源的限制,导致实验数据不充分,使方程组无解．本文使用三次样条方法,对26例临床、病理资料完备的具有淋巴结转移的乳腺癌基因表达数据进行插值处理,使表达数据满秩,从而使用最小二乘法解出加权矩阵,构建初步的表达基因调控网络．通过对构建的基因网络的初步分析表明:乳腺癌转移的形成是由多基因异常引起多条传导通路异常,致使细胞恶性转化的结果,这与生物学上公认的看法是相一致的．因此,利用此线性模型方法对基因表达谱进行分析兵有一定可行性,在认识乳腺癌转移机制,乳腺癌诊断和治疗方面具有一定的理论和应用价值．     

海洋浮游植物丰度的空间插值优化

在探索性空间数据分析(Exploratory spatial data analysis)和数据转化的基础上,利用反距离加权(Inverse distance weighting,IDW)、径向基函数(Radial basis functions,RBF)、普通克里格(Ordinary Kriging,OK),3种插值方法,对2003年8月获得的珠江口浮游植物丰度数据进行插值运算,并对插值准确度进行交叉验证。结果显示,珠江口浮游植物丰度数据具有离散性大、存在极大和极小值、呈正偏分布等特点。而对数转化能大大减小数据的离散性和不对称性,有效消除插值结果图中各类插值噪音。交叉验证显示,插值精确度OK最高,RBF次之,IDW最低。观察插值结果等值面图,发现3种方法均能较客观地模拟出浮游植物丰度的总体分布趋势,在对局部趋势的模拟上,OK的表现最好。综合评定,OK为最适合珠江口浮游植物丰度数据的插值方法。半变异模型的选择对OK的插值结果影响不明显。在四种半变异模型中,圆形模型的拟合效果最好。     

Cubic-spline interpolation to estimate effects of inbreeding on milk yield in first lactation Holstein cows

Milk yield records (305d, 2X, actual milk yield) of 123,639 registered first lactation Holstein cows were used to compare linear regression (y = β(0) + β(1)X + e), quadratic regression, (y = β(0) + β(1)X + β(2)X(2) + e) cubic regression (y = β(0) + β(1)X + β(2)X(2) + β(3)X(3) +e) and fixed factor models, with cubic-spline interpolation models, for estimating the effects of inbreeding on milk yield. Ten animal models, all with herd-year-season of calving as fixed effect, were compared using the Akaike corrected-Information Criterion (AICc). The cubic-spline interpolation model with seven knots had the lowest AICc, whereas for all those labeled as "traditional", AICc was higher than the best model. Results from fitting inbreeding using a cubic-spline with seven knots were compared to results from fitting inbreeding as a linear covariate or as a fixed factor with seven levels. Estimates of inbreeding effects were not significantly different between the cubic-spline model and the fixed factor model, but were significantly different from the linear regression model. Milk yield decreased significantly at inbreeding levels greater than 9%. Variance component estimates were similar for the three models. Ranking of the top 100 sires with daughter records remained unaffected by the model used.