Testing different 3D techniques using geometric morphometrics: Implications for cranial fluctuating asymmetry in humans

This study aimed to test the performance of 3D digitizer, CT scanner, and surface scanner in detecting cranial fluctuating asymmetry. Sets of 32 landmarks (6 in the midline and 13 bilateral) were acquired from 14 archeological crania using a 3D digitizer, and from 3D models generated from a CT scanner and surface scanner using Viewbox 4. Levels of shape variation were analyzed in MorphoJ using Procrustes analysis of variance and Principal component analysis. Intra-observer error accounted for 1.7%, 1.8%, and 4.5% of total shape variation for 3D digitizer, CT scanner, and surface scanner respectively. Fluctuating asymmetry accounted for 15%–16% of total shape variation. Variation between techniques accounted for 18% of total shape variation. We found a higher level of missing landmarks in our surface scan data than for both 3D digitizer and CT scanner data, and both 3D model-based techniques sometimes obscured taphonomic damage. All three 3D techniques are appropriate for measuring cranial fluctuating asymmetry. We advise against combining data collected with different techniques.     

Variable selection in nonlinear function-on-scalar regression

We develop a new method for variable selection in a nonlinear additive function-on-scalar regression (FOSR) model. Existing methods for variable selection in FOSR have focused on the linear effects of scalar predictors, which can be a restrictive assumption in the presence of multiple continuously measured covariates. We propose a computationally efficient approach for variable selection in existing linear FOSR using functional principal component scores of the functional response and extend this framework to a nonlinear additive function-on-scalar model. The proposed method provides a unified and flexible framework for variable selection in FOSR, allowing nonlinear effects of the covariates. Numerical analysis using simulation study illustrates the advantages of the proposed method over existing variable selection methods in FOSR even when the underlying covariate effects are all linear. The proposed procedure is demonstrated on accelerometer data from the 2003–2004 cohorts of the National Health and Nutrition Examination Survey (NHANES) in understanding the association between diurnal patterns of physical activity and demographic, lifestyle, and health characteristics of the participants.     

Patterns of intraspecific variation inAntennaria alborosea,A. corymbosa,A. marginata,A. microphylla,A. parvifolia,andA. umbrinella (Asteraceae:Inuleae)

Patterns of intraspecific variation were examined inAntennaria alborosea A. E. Porsild,A. corymbosa E. Nels,A. marginata Greene,A. microphylla Rydb.,A. parvifolia Nutt., andA. umbrinella Rydb. AlthoughA. alborosea was initially considered arctic in distribution, it became apparent that a southern montane element also exists. Our results suggest that morphological differences between arctic and southern montane specimens represent clinal variation. The additional morphological data for specimens that occur more than 1,500 km south of the species' range as it was initially described result in a better understanding of this once presumed arctic taxon. Morphological variation in the dioecious speciesA. corymbosa, A. marginata, A. microphylla, A. parvifolia, andA. umbrinella was greater between the genders than was geographic variation within each gender. These results demonstrate that both pistillate and staminate specimens must be examined in dioecious species ofAntennaria if morphological variation in the respective species is to be fully understood. Character size or number of broadly distributed species (A. microphylla andA. parvifolia) generally decreased with increasing longitude, whereas characters of species with more restricted distributions (A. alborosea, A. corymbosa, andA. marginata) generally increased in size or number with increasing latitude or longitude.Antennaria umbrinella was an exception in this respect.     

Using principal component analysis and support vector machine to predict protein structural class for low-similarity sequences via PSSM

The accurate identification of protein structure class solely using extracted information from protein sequence is a complicated task in the current computational biology. Prediction of protein structural class for low-similarity sequences remains a challenging problem. In this study, the new computational method has been developed to predict protein structural class by fusing the sequence information and evolution information to represent a protein sample. To evaluate the performance of the proposed method, jackknife cross-validation tests are performed on two widely used benchmark data-sets, 1189 and 25PDB with sequence similarity lower than 40 and 25%, respectively. Comparison of our results with other methods shows that the proposed method by us is very promising and may provide a cost-effective alternative to predict protein structural class in particular for low-similarity data-sets.     

基于RSEI模型的昆明市生态环境质量动态监测

利用遥感技术进行生态环境监测有利于快速了解生态环境的变化过程。以昆明市为研究区,以Landsat TM和OLI影像为数据源,采用主成分分析法,运用集成于绿度、湿度、干度和热度4个指标的遥感生态指数(remote sensing ecological index,RSEI),对昆明市2000—2018年生态环境质量进行了评价。结果表明:RSEI指数能较好地指示区域生态环境状况,研究区RSEI主要是受干度的影响,其次是湿度和绿度,热度对RSEI模型的影响最小; 2000—2018年,昆明市RSEI 5年平均值为0.51,生态环境质量处于一般状态(0.4～0.6),生态环境质量呈现"上升-下降-上升-下降"的波动变化趋势。其中,2010年受干旱因素影响,生态环境质量较其他年份相对较低;昆明市生态环境质量西部优于东部,其中以西南角的生态环境质量最佳。     

不同种植模式花椒园昆虫群落的结构及稳定性

对云南昭通市4种不同种植模式花椒园（花椒-玉米-大豆园、花椒-大豆园、花椒-玉米园、花椒园）昆虫群落的组成和结构进行调查,采用群落特征指数和主分量分析法对不同种植模式花椒园昆虫群落特征及其稳定性进行了研究.结果表明：研究区花椒园共发现326种昆虫;与单一种植花椒园相比,间作套种作物花椒园昆虫群落的丰富度指数、多样性指数和均匀度指数均较高,而优势度指数较低;不同种植模式花椒园昆虫群落多样性指数值大小依次为花椒玉米大豆园>花椒大豆园>花椒玉米园>花椒园.花椒、玉米、大豆间作套种系统中昆虫群落的稳定性较好.     

Insight into genetic relation and diversity of cultivated and semi-domesticated under-utilized Crotalaria species gained using start codon targeted (SCoT) markers

To augment conventional crop improvement approaches in cultivated sunnhemp (Crotalaria juncea L.) and other under-utilized Crotalaria species, genetic diversity of 94 genotypes from seven Crotalaria species was studied using 20 Start Codon Targeted (SCoT) markers. High allele number (1.32), polymorphism information content (0.37) and resolving power (6.59) established SCoT as a reliable marker system for genetic analysis in Crotalaria. All the species except Crotalaria retusa L. exhibited high number of SCoT amplicons. Analysis of molecular variance revealed significant variability between (24.0%) the species as well as within species (76.0%). A cluster analysis identified distinct groups corresponding to the seven species and also identified sub-groups within the species. The sunnhemp cultivars were distant from the landraces, suggesting the need of population improvement using distantly related genotypes. Species relationship identified Crotalaria pallida Aiton to be a close relative of C. juncea. The results of principal coordinate analysis were comparable to that of cluster analysis, revealing high genetic variability in sunnhemp and other semi-domesticated Crotalaria species. The study further suggests some measure for conservation of genetic resources and genetic improvement of these species based on the results of diversity analysis.     

东乡野生稻BILs群体耐低氮性表型性状指标筛选及其综合评价

为了鉴定东乡野生稻及其后代群体的耐低氮性,研究低氮和正常氮2种处理下“协青早B//东乡野生稻/协青早B”BC₁-F₁₂回交重组自交系株高、抽穗期、穗长、有效穗数、穗实粒数、穗总粒数、着粒密度、结实率、千粒重和单株产量等10个表型性状,利用主成分分析和模糊隶属函数对BILs群体的耐低氮性进行综合评价.结果表明： 株系116、143和157的耐低氮性强,可作为东乡野生稻耐低氮性遗传研究和水稻耐低氮性育种的中间材料.采用逐步回归分析法建立了耐低氮性最优回归方程,筛选到株高、穗总粒数、结实率、千粒重和单株产量等5个性状相对值可作为水稻全生育期耐低氮性的综合评价指标.因此,在水稻耐低氮性遗传改良中,应注重对这5个性状,尤其是穗总粒数和单株产量相对值的选择.
     

南药立体经营模式土壤质量综合评价

为筛选优化的南药立体经营模式,本试验选用适宜南方种植的4种药用植物,采用随机区组设计,在已有的杉木林下,构建4种林药立体经营模式,分别是杉木（Cunninghamia lanceolata）+梅叶冬青（Ilex asprella）+艾纳香模式（Blumea balsamifera）（简称SMA）、杉木+梅叶冬青+广金钱草（Desmodium styracifolium）模式（简称SMG）,杉木+梅叶冬青+草珊瑚（Sarcandra glabra）模式（简称SMC）,杉木+梅叶冬青模式（SM））,以杉木纯林（简称CK）为对照,分析不同模式内0~20和20~40 cm土层土壤理化性质和土壤酶活性变化,并运用主成分分析法综合评价模式对林地土壤质量的影响。结果表明（1）与对照（纯林）相比,4种林药模式下的土壤容重均显著下降,且随土层深度的增加而增加。0~20 cm土层各模式土壤容重降幅分别为：模式SMA13.4%、模式SMG 14.1%、模式SMC 20.8%和模式SM 22.3%、;20~40 cm土层的土壤容重各处理降幅为7.0%~15.5%。各模式土壤质量含水量、田间持水量、毛管持水量、毛管孔隙度和总孔隙度均显著提高（P<0.05）,且随土层深度的增加而减小,0~20 cm土层,均是以模式SM最大,分别比对照提高54.9%、100.1%、88.6%、44.9%和36.8%;20~40 cm土层,均以模式SMG最大,分别是对照的61.5%、67.6%、69.7%、43.4%和44.0%。（2）0~20 cm土层pH呈下降趋势,降幅0.7%~6.2%,20~40 cm土层中各处理pH差异较大,但均未达到显著水平。除全钾外,其余土壤养分含量各模式均随着土层深度的增加而降低。0~20 cm土层中,有机质、全氮、全磷、速效氮磷钾、交换性钙和镁以及阳离子交换量均以模式SMC含量最高,分别比对照提高79.7%、69.5%、30.3%、91.4%、279.4%、166.1%、91.6%、677.0%和70.3%。全钾含量以模式SMG最高,比对照增加了26.9%。（3）各处理土壤酶活性均随着土层深度的增加而降低。在0~20 cm土层中,与对照相比,各模式土壤的脲酶、蔗糖酶、多酚氧化酶和酸性磷酸活性差异显著（P<0.05）,其中脲酶和多酚氧化酶活性以模式SMC活性最高,分别是对照的1.7倍和1.6倍,蔗糖酶活性各模式皆低于对照,降幅59.3%~69.4%;酸性磷酸酶活性模式SMA最高,比对照提高78.7%。20~40 cm土层中,各模式及对照间仅酸性磷酸酶活性差异达到显著水平。（4）南药立体经营模式对土壤质量影响的综合排序为,模式SMC（2.811）>模式SMG（1.293）>模式SMA（0.111）>模式SM（-1.544）>CK（-2.671）。     

渭河丰、枯水期底栖动物群落特征及综合健康评价

以渭河为研究范例,分别于丰水期(2011年10月)和枯水期(2012年4月)对渭河全流域范围内45个样点的底栖动物群落进行跟踪调查,并在此基础上应用丰、枯水期底栖动物生物完整性评价指数(B-IBI)对渭河流域水生态系统进行综合健康评价。结果表明,渭河流域底栖动物群落结构具有明显的空间异质性,枯水期底栖动物群落结构单一,物种数量、生物量和香农多样性明显少于丰水期,但单位密度差异不显著。综合健康评价结果表明,渭河上游、洛河中上游地区的健康状况较好,而渭河中下游、泾河全流域及洛河下游地区的健康状况较差。相关分析显示,渭河全流域范围内丰水期和枯水期底栖动物群落的B-IBI得分呈现明显的正相关性,表明在不同水文过程时期,渭河全流域大尺度范围内底栖动物群落的生物完整性特征较为一致。在河流丰、枯水期,底栖动物群落结构的变化趋势并对比分析了渭河流域不同区域水生态系统健康水平差异的原因。